title: ACUTE_EtOH_ZT20_3

status: Public on Nov 30 2019

type: SRA

city: New York

first: Sanam

last: Shahid

state: New York

address: 1275 York Avenue

department: Department of Pediatrics

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: transcriptomic

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Eland2e was  for mapping to the mouse mm10 reference genome.
Cufflinks2 was used for RNA quantification.
BioCycle was used to determine oscillating transcripts at a pval < 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: tsv files containing statistical significance of transcript oscillation and rpkm per timepoint and replicate.

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA was extracted from the liver with TRIzol (Invitrogen), followed by precipitation with isopropanol and ethanol.
RNA libraries for each group were prepared as described in the TruSeq RNA Sample Preparation v2 Guide (Illumina).

tag: strain

tag: Sex

value: male

tag: genotype

value: wild type


title: ACUTE_EtOH_ZT20_2


title: ACUTE_EtOH_ZT20_1


title: ACUTE_EtOH_ZT16_1


title: ACUTE_EtOH_ZT12_3


title: ACUTE_EtOH_ZT16_2


title: ACUTE_EtOH_ZT12_2


title: ACUTE_EtOH_ZT12_1


title: ACUTE_EtOH_ZT8_3


title: ACUTE_EtOH_ZT8_1


title: ACUTE_EtOH_ZT8_2


title: ACUTE_EtOH_ZT4_3


title: si-uc.323-1

type: RNA

city: Guangzhou

first: Yu

last: Sun

address: 58 Zhongshan Road 2

country: China

institute: the First Affiliated Hospital of Sun Yat-Sen University

hyb_protocol: Then heated the mixture at 60°C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner(G2505C) using one color scan for 4×180k array slides (Scan Area 61×21.6mm，Scan resolution 3um，Dye channel is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment

organism: Rattus norvegicus

source_name: Gene expression after 24h of si-uc.323 transfection in cardiomyocytes

label_protocol: Total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer.

growth_protocol: Primary cultures of NRVMs were prepared under aseptic conditions from 1-to 2-day-old Sprague-Dawley rats obtained from the Experimental Animal Facility of Sun Yat-sen University. First, the hearts were excised from the rats, and the adipose, atrial and blood vessel tissue was separated from the ventricles, which were placed in D-Hanks solution. Then, the ventricle tissue was cut into 2 mm3 pieces and dissociated in 0.125% trypsin at 37°C for 5 minutes. The cell suspensions were separated, immersed again in D-Hanks solution three times, redigested in 0.05% collagenase at 37℃ for 2.5 hours, and neutralized with equal volumes of DMEM containing 10% NBS. The cell suspensions were then collected by centrifugation at 510 rpm for 8 minutes. The suspensions were separated and dipped in D-Hanks solution. After this step was repeated twice, the isolated cells were resuspended in DMEM containing 10% NBS and preplated for 1 hour to remove fibroblasts. Unattached NRVMs in DMEM containing 10% NBS and 1% 5-bromodeoxyuridine (5-BrdU) were plated at a density of 1×106 cells/well in 6-well plates and incubated in a humidified atmosphere of 95% air/5% CO2 at 37℃.

extract_protocol: RNA was extracted bymirVanaTM RNA isolation Kit （Applied Biosystem p/n AM1556） following the manufacturers instructions.

treatment_protocol: siRNA transfection was performed using Lipofectamine™ RNAiMAX (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. The sequence of the siRNA targeting uc.323 (si-uc.323) was: 5′-GGUAAGUAAUUUCAGCAAU dTdT-3′. After 36 hours of culture, scrambled siRNA (si-scramble) (50 nmol/L) or si-uc.323 (50 nmol/L) in serum-free medium was added to each well, and the cells were incubated for 3 hours.

value: Sprague-Dawley

tag: age

value: 1-2 days

tag: tissue

value: heart

tag: cell type

value: primary neonatal rat ventricular myocytes (NRVM)

tag: genotype/variation


title: WT Sham mouse-4

hyb_protocol: 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 9 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: Gene expression after 4 weeks of sham surgery in mouse heart

label_protocol: each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.

growth_protocol: Eight-to ten-week-old male C57BL/6J mice weighing 24–26 g were used in our research.

treatment_protocol: The mice were anaesthetized by the intraperitoneal injection of 1.5% pentobarbital  and underwent descending aortic banding , which was performed using the following procedure: after the animals were anesthetized, the descending aorta was banded with a 7-0 silk suture. A bent 26-gauge needle was used to ligate the aorta and was quickly removed after the procedure. A similar surgery was performed in sham-operated mice.

value: 8-10 weeks

tag: gender

tag: treatment

value: sham surgery


title: si-scramble-1

source_name: Gene expression after 24h of si-scramble transfection in cardiomyocytes

value: scrambled siRNA (si-scramble)


title: WT Sham mouse-2


title: ACUTE_EtOH_ZT4_2


title: WT Sham mouse-1


title: WT AB mouse-4

source_name: Gene expression after 4 weeks of aortic banding surgery in mouse heart

value: aortic banding surgery


title: ACUTE_EtOH_ZT4_1


title: ACUTE_EtOH_ZT1_3


title: ACUTE_EtOH_ZT16_3


title: si-uc.323-3


title: si-uc.323-2


title: ACUTE_CTRL_ZT20_2


title: ACUTE_CTRL_ZT20_3


title: ACUTE_EtOH_ZT1_1


title: WT AB mouse-3


title: si-scramble-3


title: si-scramble-2


title: ACUTE_EtOH_ZT1_2


title: WT AB mouse-2


title: WT Sham mouse-3


title: ACUTE_CTRL_ZT20_1


title: ACUTE_CTRL_ZT16_3


title: ACUTE_CTRL_ZT16_2


title: WT AB mouse-1


title: ACUTE_CTRL_ZT16_1


title: ACUTE_CTRL_ZT12_3


title: HSV1 infected RPF replicate 2

city: Ottawa

first: Tommy

last: Alain

state: Ontario

address: 401 Smyth Road

country: Canada

institute: Children's Hospital of Eastern Ontario Research Institute

description:
ribosome protected fragment (RPF)
308

data_processing:
adapter sequence was removed using FASTX
reads mapping to rDNA with Bowtie 2 were discarded
Bowtie 2 (allowing up to 1 mismatches) was used to map reads and uniquely mapped reads with MAPQ score >=10 were carried forward
Wig files were then generated by summing the numbers of reads obtained from each position in the human genome. For this, each read was counted once.
Unique reads mapping to the CDS of RefSeq transcripts were counted and used to calculate RPKM based on the total reads per sequencing run
Genome_build: mm9
Supplementary_files_format_and_content: CSV file containing RNA and RPF RPKM, as well as Translation efficiency (TE; RPF/RNA) for all treatments and replicates.

source_name: breast cancer cell model

growth_protocol: 4T1 cells were grown in RPMI1640 media (Fisher) supplemented with 10% fetal bovine serum (Wisent Bioproducts) and 0.1% penicillin and streptomycin.

extract_protocol:
Cells were lysed in polysome buffer. One portion of the lysate was used to prepare RPF mRNA, while the other portion of lysate was used to purify poly(A)+ mRNA. Poly(A)+ was enriched from total mRNA using magnetic oligo-dT DynaBeads and subjected to alkaline fragmentation. Fragmented mRNAs were size-selected on a denaturing 10% polyacrylamide-urea gel and the bands corresponding to 30–50 nucleotides were excised, eluted, and precipitated with isopropanol. For isolation of RPF mRNA, lysates were subjected to digestion with Rnase I. Monosomes were pelleted by ultracentrifugation. Ribosome protected fragments of mRNA were size-selected via gel purification.
Fragmented total mRNA or size-selected RPF mRNA was dephosphorylated, ligated, and reverse-transcribed. The resulting cDNA was circularized, rRNA contamination was reduced by subtractive hybridization, and the resulting library was PCR amplified using indexed primers.

treatment_protocol: Cells were infected with the indicated virus at a dose where 50% of cells were viable after 48 hours. The cells were harvested for RNA- and RPF-Seq at 18 hours post-infection.

tag: cell line

tag: tissue source

value: mammary gland

tag: background strain

tag: timepoint

value: 18 hours post-infection

tag: infection

value: HSV1 infected


title: ACUTE_CTRL_ZT12_2


title: ACUTE_CTRL_ZT12_1


title: ACUTE_CTRL_ZT8_3


title: ACUTE_CTRL_ZT8_1


title: HSV1 infected mRNA replicate 2

description:
total mRNA
307


title: ACUTE_CTRL_ZT4_3


title: ACUTE_CTRL_ZT8_2


title: ACUTE_CTRL_ZT4_1


title: VACV infected mRNA replicate 2

description:
total mRNA
305

value: VACV infected


title: ACUTE_CTRL_ZT4_2


title: ACUTE_CTRL_ZT1_1


title: Reovirus infected RPF replicate 2

description:
ribosome protected fragment (RPF)
304

value: Reovirus infected


title: CHRONIC_EtOH_ZT20_2


title: ACUTE_CTRL_ZT1_2


title: ACUTE_CTRL_ZT1_3


title: CHRONIC_EtOH_ZT16_3


title: Reovirus infected mRNA replicate 2

description:
total mRNA
303


title: CHRONIC_EtOH_ZT16_2


title: CHRONIC_EtOH_ZT20_3


title: mock infected mRNA replicate 2

description:
total mRNA
301

value: mock infected


title: mock infected RPF replicate 2

description:
ribosome protected fragment (RPF)
302


title: CHRONIC_EtOH_ZT16_1


title: CHRONIC_EtOH_ZT12_3


title: HSV1 infected RPF replicate 1

description:
ribosome protected fragment (RPF)
208


title: HSV1 infected mRNA replicate 1

description:
total mRNA
207


title: CHRONIC_EtOH_ZT12_2


title: VACV infected RPF replicate 2

description:
ribosome protected fragment (RPF)
306


title: VACV infected RPF replicate 1

description:
ribosome protected fragment (RPF)
206


title: CHRONIC_EtOH_ZT12_1


title: CHRONIC_EtOH_ZT8_1


title: CHRONIC_EtOH_ZT4_3


title: VACV infected mRNA replicate 1

description:
total mRNA
205


title: CHRONIC_EtOH_ZT8_2


title: CHRONIC_EtOH_ZT20_1


title: Reovirus infected RPF replicate 1

description:
ribosome protected fragment (RPF)
204


title: CHRONIC_EtOH_ZT0_2


title: CHRONIC_EtOH_ZT4_2


title: CHRONIC_EtOH_ZT0_3


title: CHRONIC_EtOH_ZT4_1


title: CHRONIC_CTRL_ZT20_1


title: mock infected RPF replicate 1

description:
ribosome protected fragment (RPF)
202


title: CHRONIC_CTRL_ZT12_3


title: mock infected mRNA replicate 1

description:
total mRNA
201


title: CHRONIC_CTRL_ZT16_1


title: CHRONIC_CTRL_ZT16_3


title: CHRONIC_CTRL_ZT20_3


title: CHRONIC_CTRL_ZT12_2


title: CHRONIC_CTRL_ZT12_1


title: CHRONIC_CTRL_ZT16_2


title: CHRONIC_EtOH_ZT8_3


title: CHRONIC_CTRL_ZT20_2


title: CHRONIC_CTRL_ZT8_2


title: CHRONIC_CTRL_ZT4_3


title: CHRONIC_CTRL_ZT8_3


title: CHRONIC_CTRL_ZT4_2


title: Reovirus infected mRNA replicate 1

description:
total mRNA
203


title: CHRONIC_CTRL_ZT0_2


title: CHRONIC_CTRL_ZT0_1


title: CHRONIC_CTRL_ZT4_1


title: CHRONIC_CTRL_ZT0_3


title: CHRONIC_EtOH_ZT0_1


title: Input genomic DNA, NCI-H209

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

description: input genomic DNA used for peak calling by MACS2

library_source: genomic

data_processing:
Reference files of the human reference sequence assembly (NCBI Build 37/hg19, February 2009) and GTF annotation file were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html)
ChIP-seq reads were trimmed down to 50 bp and were aligned using Bowtie (version 1.1.0) (Langmead et al., 2009) with the command “-S -a --best --strata -v 1 -m 1”.
BAM files were sorted using Picard SortSam (http://picard.sourceforge.net/).
TTF-1 or ASCL1 binding regions were identified using MACS2 software (Model based analysis of ChIP-seq) (version 2.0.9) (Zhang et al, 2008) with a default q-value threshold of 0.00001.
WIG to bigWig conversion was performed  using UCSC wigToBigWig.
To reduce the size of the bigWig files, regions with value less than 2 were removed using bwtool (Pohl and Beato, 2014) with the command "remove less 2".
Genome_build: hg19
Supplementary_files_format_and_content: BED and WIG files were generated using MACS2 (version 2.0.9).

molecule: genomic DNA

organism: Homo sapiens

source_name: A small cell lung carcinoma cell line, NCI-H209

growth_protocol: NCI-H209 was obtained from ATCC, and maintained as reccomended. Briefly, H209 cells were cultured at 37℃ and 5% CO2 in RPMI 1640 medium (Gibco, Thermo Fisher Scientific) supplemented with 10% (v/v) fetal bovine serum (FBS) (HyClone, GE Healthcare Life Sciences, Piscataway, NJ, USA) and 100 U/ml penicillin-streptomycin (Gibco).

extract_protocol:
ChIP-seq of H209 cells were performed using 5 μg of anti-TTF-1 antibody (#MS-699-P, Lab Vision Corporation, Fremont, CA, USA) or anti-ASCL1 antibody (#556604, BD Biosciences, Franklin Lakes, NJ, USA) as described previously (Koinuma D et al, Mol cell biol, 2009).
The libraries were constructed as described (Murai et al, Cell Discov, 2015), using IonXpress Plus Fragment Library Kit (Thermo Fisher Scientific). Adaptor-ligated samples were amplified by 15 cycles of PCR and purified by E-Gel SizeSelect (Thermo Fisher Scientific).

treatment_protocol: untreated

tag: small cell lung carcinoma subtype

value: classic type SCLC

value: untreated

tag: antibody


title: Input genomic DNA, NCI-H441, replicate 2

description: input genomic DNA used for peak calling of replicate 2

data_processing:
Reference files of the human reference sequence assembly (NCBI Build 37/hg19, February 2009) and GTF annotation file were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html)
ChIP-seq reads were trimmed down to 50 bp and were aligned using Bowtie2 (version 2.2.6) (Langmead et al., 2009) with the command “-S -q --local -x”.
BAM files were sorted using Picard SortSam (http://picard.sourceforge.net/).
TTF-1 and ASCL1 binding regions were identified using MACS2 software (Model based analysis of ChIP-seq) (version 2.1.0.20151222) (Zhang et al, 2008) with a default q-value threshold of 0.00001.
bdg(WIG) to bigWig conversion was performed  using bedClip and bedGraphToBigWig.
To reduce the size of the bigWig files, regions with value less than 2 were removed using bwtool (Pohl and Beato, 2014) with the command "remove less 2".
Genome_build: hg19
Supplementary_files_format_and_content: BED and BDG(WIG) files were generated using MACS2 (version 2.1.0.20151222). BDG files were converted to bigwig format by bedGraphToBigWig.

source_name: A lung adenocarcinoma cell line, NCI-H441

growth_protocol: NCI-H209 and NCI-H441 were obtained from ATCC, and maintained as reccomended. Briefly, both cells were cultured at 37℃ and 5% CO2 in RPMI 1640 medium (Gibco, Thermo Fisher Scientific) supplemented with 10% (v/v) fetal bovine serum (FBS) (HyClone, GE Healthcare Life Sciences, Piscataway, NJ, USA) and 100 U/ml penicillin-streptomycin (Gibco).

extract_protocol:
ChIP-seq of H209 and H441 cells were performed using 5 μg of anti-TTF-1 antibody (#MS-699-P, Lab Vision Corporation, Fremont, CA, USA) or anti-ASCL1 antibody (#556604, BD Biosciences, Franklin Lakes, NJ, USA) as described previously (Koinuma D et al, Mol cell biol, 2009).
The libraries were constructed as described (Murai et al, Cell Discov, 2015), using IonXpress Plus Fragment Library Kit (Thermo Fisher Scientific). Adaptor-ligated samples were amplified by 15 cycles of PCR and purified by E-Gel SizeSelect (Thermo Fisher Scientific).

value: adenocarcinoma

tag: chip antibody


title: HT-29-siIGF-1R

city: Beijing

first: shuqing

last: wang

address: No.10, You An Men Wai, Fengtai.

institute: Capital Medical University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to GRCh38  genome using Mapsplice v2.1.8 with  parameters -s 22 -p 15 --ins 6 --del 6 --non-canonical --bam -o
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: human colorectal adenocarcinoma cell

growth_protocol: Human colonic cancer cell lines HT-29bwas purchased from China Cell Bank (authorized by ATCC). Cells were grown in RPMI 1640 medium containing 10% fetal bovine serum at 37°C in a humid atmosphere (5% CO2).

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA library using standard Ion proton RNA-Seq Kit v2.0 protocol

treatment_protocol: Cells grown in 3.5cm dishes were routinely transfected with siIGF-1R (5′-GCCGACACUACUACUACAATT-3′)

value: transfected with siIGF-1R

tag: source

value: from the primary tumor of a 44-year-old Caucasian female with colorectal adenocarcinoma.


title: TTF-1 binding region in NCI-H209, replicate 2

description: anti-TTF-1 ChIP-seq


title: TTF-1 binding region in NCI-H441, replicate 2

description: anti-TTF-1 ChIP-seq


title: HT-29


title: ASCL1 binding region in NCI-H209, replicate 2

description: anti-ASCL1 ChIP-seq


title: H9_RSeT_nEnd_R1

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: DanStem

country: Denmark

institute: Copenhagen University

data_processing:
Reads were mapped using STAR, removing multi-mappers
Count tables were generated using quantMode
Genome_build: hg38
Supplementary_files_format_and_content: counts

source_name: Human embryonic stem cells

growth_protocol: Conventional pluripotent stem cells were grown in KOSR medium supplemented with 10ng/mL FGF2. Naïve pluripotent stem cells were grown in N2B27 medium supplemented with either a. 10ng/mL LIF, 1µM CHIR99021, 1µM PD0325901 and 2µM Gö6983 or b. 10ng/mL LIF, 1µM CHIR99021 and 1µM PD173074. Extra-embryonic endoderm was differentiated in RPMI GlutaMAX with B27 minus insulin and grown in N2B27 medium supplemented with 10ng/mL LIF, 3µM CHIR99021 and 100ng/mL Activin A. Endoderm was grown in either a. N2B27 supplemented with 10ng/mL LIF, 3µM CHIR99021 and Activin A or b. According to the Materials and Methods section in Cheng et al. (2012).

extract_protocol:
Total RNA was collected using the RNeasy Mini Kit (Qiagen). Genomic DNA was eliminated by Dnase treatment (Qiagen).
Ribosomal RNA was removed using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). Sequencing libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB)

tag: background

value: Extra-embryonic endoderm

tag: Stage

value: Embryonic


title: H9_RSeT_nEnd_R2


title: H9_RSeT_PrE_R2-2


title: H9_DE_R3

value: Endoderm


title: H9_RSeT_PrE_R1-2


title: H9_RSeT_nEnd_R3


title: H9_DE_R1


title: HUES4_ADE_R2


title: H9_t2iLGo_nEnd_R3


title: HUES4_ADE_R1


title: H9_RSeT_nES_R1

value: Naive pluripotent stem cells


title: H9_RSeT_PrE_R1-1


title: H9_t2iLGo_nEnd_R1


title: H9_ADE_R2


title: CHRONIC_CTRL_ZT8_1

tag: strain

tag: Sex

value: male

tag: genotype

value: wild type


title: H9_ADE_R1

tag: cell type


title: H9_RSeT_PrE_R2-1


title: H9_t2iLGo_nEnd_R2


title: HUES4_pES_R2

value: Conventional pluripotent stem cells


title: H9_RSeT_nES_R2


title: MkMP_smallRNA_rep2

city: Newark

first: Chen-Yuan

last: Kao

state: DE

address: 15 Innovation Way, Rm 243

institute: University of Delaware

description:
50-80 nt
sample name in processed data file:
MkMP16

data_processing:
Basecalling is done using bcl2fastq_1.8.3
Illumina HiSeq 2500
A custom bioinformatics pipeline was used to end-trim raw reads to obtain an average Q>30, and to partition the data into miRNA and piRNA size fractions.
trimmed and filtered reads were then clustered by identical sequence and each cluster was aligned against human miRNA sequences downloaded from the miRBase (Release 21) and grouped by mature form or to human piRNA sequences from the piRNABank using CLC Genomics Workbench (CLC Bio)
sequencing data were checked for quality control metrics using fastqc and CLC Genomics Server tools (CLC Bio) and poor quality sequence and adapters were removed. The resulting reads were mapped against Homo sapien Hg19 (GRCh37) using TopHat2 with RSeQC providing QC metrics on the reference mapping. TopHat fusion was used to detect gene fusion events. Raw counts per annotated gene and exon were extracted from aligned BAM file using HTSeq.
Supplementary_files_format_and_content: Differential expression comparison; xlsx or csv file with gene counts or count per million (CPM)

growth_protocol: CD34+ cell-derived Mks were cultured starting with frozen G-CSF-mobilized human peripheral blood CD34+ cells. Cells were cultured in IMDM supplemented with 20% BIT 9500, 100 ng/mL TPO, 100 ng/mL stem cell factor, 2.5 ng/mL IL-3, 10 ng/mL IL-6 & IL-11 and human LDL under 5% O2 for 5 days. IL-3 was increased to 10 ng/mL and IL-6 was substituted with IL-9 at day 5. Cells were cultured under 20% O2 from day 5 to 7. At day 7, CD61+ cells were enriched by using MACS separation with anti-CD61 magnetic microbeads. Enriched cells were then culture in IMDM supplemented with 20% BIT 9500, 100 ng/mL TPO, 100 ng/mL SCF, and human LDL under 20% O2 for another 5 days. Mks, MkMPs, PLPs were isolated from the culture medium of the day 12 Mk culture.

extract_protocol:
isolation protocol: Blood for isolation of human platelets (PLTs) was collected by venipuncture from adult healthy human volunteers, into a syringe with ACD buffer at a volume ratio of 1:6 (ACD:blood). Blood was centrifuged at 250 × g for 10 min and the platelet-rich plasma was isolated from the supernatant. PLTs were then pelleted at 750 × g for 10 min, followed by 1 wash with HEN buffer (10 mM HEPES, pH 6.5, 1mM EDTA, 150 mM NaCl) containing 0.05 U/ml apyrase. After that, PLTs were resuspended in HEPES-Tyrode’s buffer (137 mM NaCl, 20 mM HEPES, 5.6 mM glucose, 1 g/l BSA, 1 mM MgCl2, 2.7 mM KCl, 3.3 mM NaH2PO4).
Total RNA was isolated using the miRNeasy micro kit (Qiagen). RNA concentration was measured by NanoDrop and size distribution of total RNA was analyzed using an ABI Prism 3130XL Genetic Analyzer. Small-size RNA (18-40 nt and 40-150 nt in size) was purified by 15% polyacrylaminde/urea gels and eluted from gels for library construction using Illumina TruSeq Small RNA Sample Prep kit according to the manufacturer’s protocol. The 11 libraries described above were pooled together.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Megakaryocyte-derived microparticles

tag: rna fraction

value: small RNA

tag: replicate


title: MkMP_smallRNA_rep1

description:
50-80 nt
sample name in processed data file:
MkMP13


title: MkMP_miRNA_rep3

description:
20-30 nt
sample name in processed data file:
MkMP21

value: miRNA


title: PLP_miRNA_rep2

description:
20-30 nt
sample name in processed data file:
PLP16

source_name: Megakaryocyte-derived platelet-like particle (PLP)


title: MkMP_miRNA_rep2

description:
20-30 nt
sample name in processed data file:
MkMP16


title: PLP_miRNA_rep3

description:
20-30 nt
sample name in processed data file:
PLP21


title: PLP_miRNA_rep1

description:
20-30 nt
sample name in processed data file:
PLP13


title: PLP_smallRNA_rep2

description:
50-80 nt
sample name in processed data file:
PLP16


title: H9_h2iL_PrE_R1


title: MkMP_miRNA_rep1

description:
20-30 nt
sample name in processed data file:
MkMP13


title: PLP_smallRNA_rep1

description:
50-80 nt
sample name in processed data file:
PLP13


title: PLP_smallRNA_rep3

description:
50-80 nt
sample name in processed data file:
PLP21


title: MkMP_smallRNA_rep3

description:
50-80 nt
sample name in processed data file:
MkMP21


title: HUES4_pES_R1


title: Input genomic DNA, NCI-H209, replicate 2

tag: treatment

tag: cell line


title: H9_DE_R2


title: PLT_smallRNA_rep2

description:
20-40 nt
sample name in processed data file:
H13PLT

source_name: Platelet (PLT)

value: Human platelet


title: H9_h2iL_PrE_R3


title: PLT_lncRNA_rep1

description:
40-150 nt
sample name in processed data file:
H11PLT

value: Long non-coding RNA


title: PLT_lncRNA_rep2

description:
40-150 nt
sample name in processed data file:
H13PLT


title: H9_t2iLGo_PrE_R3


title: Mk_smallRNA_rep3

description:
20-40 nt
sample name in processed data file:
D21Mk

source_name: Megakaryocyte (Mk)

value: Human CD34+ cell-derived megakaryocyte


title: PLT_smallRNA_rep1

description:
20-40 nt
sample name in processed data file:
H11PLT


title: H9_t2iLGo_PrE_R1


title: H9_h2iL_PrE_R2


title: H9_t2iLGo_PrE_R2


title: Mk_smallRNA_rep2

description:
20-40 nt
sample name in processed data file:
D16Mk


title: H9_t2iLGo_nES_R3


title: Mk_smallRNA_rep1

description:
20-40 nt
sample name in processed data file:
D13Mk


title: Mk_lncRNA_rep2

description:
40-150 nt
sample name in processed data file:
D16Mk


title: H9_h2iL_nES_R1


title: H9_t2iLGo_nES_R2


title: Mk_lncRNA_rep1

description:
40-150 nt
sample name in processed data file:
D13Mk


title: H9_h2iL_nES_R3


title: H9_pES_R2


title: H9_h2iL_nES_R2


title: SUM149-vector control #2

city: LA

first: Madhuri

last: Wadehra

state: CA

address: 675 Charles Young Dr. South/ 4726 MRL

department: Pathology and Lab Medicine

institute: UCLA

description: SUM149-VC 2

data_processing:
Data quality check was done on an Illumina Sequencing Analysis Viewer. Demultiplexing was performed with the Illumina Bcl2fastq2 (v 2.17) program.
The STAR ultrafast universal RNA-seq aligner (v2.5.2b) was used to generate the genome index and perform alignments.  Reads were aligned to a genome index that includes both the genome sequence (GRCh38 primary assembly) and the exon/intron structure of known gene models (Gencode v22 genome annotation).  Files with aligned reads were used to generate strand-specific, gene-level count summaries with STAR's built-in read reads per gene counter. Differential expression analysis was performed with DESeq2.
Counts were normalized per-sample in units of RPKMs after correcting for gene mappable length and sample total counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: TMM_normalized_reads_count_per_million

growth_protocol: 500mL Ham’s F12K + 5% FBS + 1% Penicillin-Streptomycin (5mL) + 4ug/ml Gentamicin+ 5μg/mL Insulin + 1μg/mL Hydrocortisone

extract_protocol:
RNA was extracted using Qiagen total RNA purification as per the manufacturer’s instructions. Total RNA was quantified and 260/280 ratios determined using Nanodrop (all samples with a 260/280>1.97). 1μg of total RNA was used as starting material for each sample.
RNA sequencing and library preparation was performed by the UCLA Technology Center for Genomics and Bioinformatics with Kapa hyper Prep Kits with RiboErase. The workflow consists of rRNA depletion, cDNA generation, and end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Sequencing was performed on Illumina Hiseq for a single read 50 run.

treatment_protocol: cells stably infected with shRNA lentiviral control or knockdown vectors.

value: SUM149PT cells

value: control


title: SUM149-vector control #1

description: SUM149-VC 1


title: SUM149-EMP2 knockdown # 2

description: SUM149-KD 2

value: EMP2 knockdown


title: SUM149-EMP2 knockdown # 1

description: SUM149-KD 1


title: BM_EBF1-KO_EBF1-ER_4OHT_rep3 [Ebf1-ER+4OHT_3]

city: Lund

first: Mikael

last: Sigvardsson

address: Sölvegatan 19

country: Sweden

institute: Lund University

data_processing:
RNA-Sequencing and data analysis: Libraries  were single-end sequenced on a NexSeq500.  For analysis of RNA-Seq experiments the reads were aligned to mouse reference  genome (mm10 / GRCm38) using STAR (2.6.0b-1) (Dobin, A etal. 2012), with single read, standard settings. If not indicated, further  analyses were performed using the HOMER platform (v4.8, v4.10) (Heinz et al. 2010). For analysis of statistically significance among  differently expressed genes, the data was analyzed using analyzeRepeats.pl with the –  noadj option, followed by the getDiffExpression.pl  command using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Homer processed raw read count txt file of RNA-seq expression.

source_name: RNA-seq of Ebf1-ER transduced Ebf1-KO B-cell progenitor cultured with 4OHT

growth_protocol: Primary Ebf1-/-  BM pro-B cells (CD19+CD43+IgM-IgD)- were cultured in vitro for a week on OP9 stroma cells using Opti-MEM (ThermoFisher Scientific, Waltham, MA) supplemented with 10% heat-inactivated fetal calf serum (FCS) (HyClone, GE Healthcare, Chicago, IL), 25mM HEPES (ThermoFisher Scientific), 50mg/ml Gentamicin (ThermoFisher Scientific), 50mM β-mercaptoethanol (β-ME) (Sigma-Aldrich, St. Louis, MO), 10ng/ml KIT ligand, 10ng/ml FLT3 ligand, and 10ng/ml Interleukin-(IL-)7. All mouse cytokines were bought from PeproTech (Rocky Hill, NJ). The cultured cells were transduced either with Ebf1-pMIG or Ebf1-ER-pMIG retrovirus and  after 3 days  CD19+ cells sorted and expanded in the presence of 1uM 4 Hydroxytamoxifen (4OHT).

extract_protocol:
For RNA-seq: Total RNA was isolated by use of RNAeasy Micro Kit (Qiagen, Hilden, Germany) according to manufacturer’s recommendations.
RNA-seq: Libraries were constructed using NuGEN’s Ovation Ultralow Library systems (NuGEN Technologies, San Calros, CA) and were subsequently subjected to 76 cycles of NextSeq500 sequencing (Illumina, San Diego,CA).

treatment_protocol: For withdrawal experiment 4OHT was withdrawn from the cultures and after 72hours the CD19+ cells sorted and the extracted RNA were subsequently sequenced.

tag: strain background

tag: tissue

value: bone marrow

value: Ebf1-/- B-cell progenitor cells

tag: genotype/variation

value: Retrovirally transduced with pMiG-Ebf1-ER for stable expression of Tamoxifen dependant Ebf1


title: H9_pES_R1

value: Embryonic


title: Mk_lncRNA_rep3

description:
40-150 nt
sample name in processed data file:
D21Mk


title: H9_t2iLGo_nES_R1

value: Naive pluripotent stem cells


title: BM_EBF1-KO_EBF1-ER_4OHT_rep1 [Ebf1-ER+4OHT_1]


title: BM_EBF1-KO_EBF1-ER_4OHT_rep2 [Ebf1-ER+4OHT_2]


title: BM_EBF1-KO_EBF1-ER_4OHT_72h_withdrawal_rep2 [Ebf1-ER_72h-4OHT_2]

source_name: RNA-seq of Ebf1-ER transduced Ebf1-KO B-cell progenitor 72h 4OHT witdrawel


title: BM_EBF1-KO_EBF1_4OHT_rep3 [Ebf1-Ctl+4OHT_3]

source_name: RNA-seq of Ebf1 transduced Ebf1-KO B-cell progenitor cultured with 4OHT

value: Retrovirally transduced with pMiG-Ebf1 for stable Ebf1 expression


title: BM_EBF1-KO_EBF1_4OHT_rep2 [Ebf1-Ctl+4OHT_2]


title: BM_EBF1-KO_EBF1_4OHT_rep1 [Ebf1-Ctl+4OHT_1]


title: BM_EBF1-KO_EBF1-ER_4OHT_72h_withdrawal_rep1 [Ebf1-ER_72h-4OHT_1]


title: BM_EBF1-KO_EBF1-ER_4OHT_72h_withdrawal_rep3 [Ebf1-ER_72h-4OHT_3]


title: BM_EBF1-KO_EBF1_4OHT_72h_withdrawal_rep1 [Ebf1-Ctl_72h-4OHT_1]

source_name: RNA-seq of Ebf1 transduced Ebf1-KO B-cell progenitor 72h 4OHT witdrawel


title: BM_EBF1-KO_EBF1_4OHT_72h_withdrawal_rep3 [Ebf1-Ctl_72h-4OHT_3]


title: 24hpi_3_circRNA

city: Hong Kong

first: Hein Min

last: Tun

address: Prince of Wales Hospital, Shatin

country: Hong Kong

institute: CUHK

description: circRNA.TPM.xlsx

data_processing:
The obtained raw reads were subjected to quality assessment using fastp (0.19.5). Reads containing adapter, reads of N base over 5bp, and low-quality reads were removed to obtain clean reads of high quality.
To identify circRNA, clean reads were aligned with the human reference genome GRCh38 (http://genome.ucsc.edu/) using HISAT2 (https://bio.tools/hisat2). CIRI2  and find_circ (version 1.2) software were used for circRNA prediction. Overlapping circRNAs between the two software were preserved. The BWA method was adopted to identify miRNA. Unique sequences containing 18 to 35 nucleotides were mapped to miRBase 22.0 by BLAST search to identify known and novel miRNAs. The expression of circRNA and miRNA were normalized to tags per million counts (TPM). TPM = (actual miRNA/circRNA counts of total clean read) × 106. To identify mRNA, after alignment with the human reference genome GRCh38 with HISAT2, clean reads were quantified based on the number of reads spanning the back-splicing junction, and their fragments per kb for a million reads (FPKM) were calculated using HTSeq 0.10.0. RNAs with log2 (fold change) ≥ 1 and p ≤ 0.05 were defined as differentially expressed (DE) by DESeq2 (version 1.18.1).
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM value of mRNA, and TPM value of miRNA and circRNA for all conditions in xls format

source_name: Calu-3 cells

growth_protocol: Calu-3 cells were maintained in Dulbecco’s Modified Eagle Medium/F12 (DMEM/F12) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 100 U/ml penicillin and 100 µg/ml streptomycin.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol, followed by DNase I digestion (Epicentre) for 15 min at 37°C.
An rRNA-depleted, RNaseR treated RNA library, a small RNA library, and a mRNA library were constructed for the identification of circRNA, miRNA, and mRNA, respectively. To prepare for circRNA sequencing, total RNA was treated by RNase R (RNR07250, Epicentre) for 20 min at 37°C, followed by rRNA depletion using a Ribo-Zero Gold Kit (Epicentre) under the manufacturer’s recommendations. After purification, the RNA product was fragmented using VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme), along with total RNAs used for both miRNA and mRNA sequencing separately.

treatment_protocol: Calu-3 cells were mock infected or infected with MERS-CoV at 4 MOI and incubated in DMEM medium. Cell pellets were harvested at 6 and 24 hours post infection.

value: lung adenocarcinoma

value: Calu-3 cells

tag: passage

tag: infection

value: MERS-CoV at 4 MOI


title: 24hpi_2_circRNA

description: circRNA.TPM.xlsx


title: 6hpi_3_circRNA

description: circRNA.TPM.xlsx


title: Mock_3_circRNA

description: circRNA.TPM.xlsx

value: mock


title: BM_EBF1-KO_EBF1_4OHT_72h_withdrawal_rep2 [Ebf1-Ctl_72h-4OHT_2]


title: 6hpi_1_circRNA

description: circRNA.TPM.xlsx


title: 6hpi_2_circRNA

description: circRNA.TPM.xlsx


title: Tam

city: Los Angeles

first: Byoung San

last: Moon

state: California

address: 1425 San Pablo St. 409B

institute: University of Southern California

data_processing:
The generated fastq files were aligned to the UCSC mouse reference genome assembly mm9 using TopHat.
The TopHat program used high-throughput short read aligner Bowtie to align the reads to the reference genome.
The aligned reads were processed by Cufflinks 2.0.0. Relative abundance of transcript was measured by Fragments Per Kilobase of exon per Million mapped fragments (FPKM).
The GTF annotation files for UCSC mm9 was used for gene annotation.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values

source_name: E14 mouse embryonic stem cells

growth_protocol: E14 mouse ES cells were grown in ESC media containing GMEM with 15% FBS, 1% NEAA, 1% Sodium Pyruvate, 1% L-glutamine, 1% PenStrep, 1X B-mercaptoethanol, and 1000U LIF. Cells were passaged using 0.05% Trypsin in PBS solution.

extract_protocol:
Total RNA was extracted from the cells using Trizol reagent
RNA libraries were prepared for sequencing using TruSeq stranded RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries

treatment_protocol: E14 mouse ES cell lines with loxP flanked Oct4 DE and transgenic mOct4 were treated with 4-OH tamoxifen or 4-OH tamoxifen and doxycycline for 48 hours

value: pluripotent stem cell

tag: construct

value: Doxycycline inducible

value: Tamoxifen inducible


title: 24hpi_1_circRNA

description: circRNA.TPM.xlsx


title: DoxTam


title: WT


title: High glucose +PJ34

city: Jinan

first: Mingxiang

last: Zhang

state: China

address: 107, jinan culture road

department: Department of Cardiology

institute: Qilu Hospital of Shandong University

description: High glucose +PJ34

hyb_protocol: After fragmentation, each sample was hybridized onto a GeneChip™ Human Transcriptome 2.0 Array (Thermo Fisher Scientific). The procedure was conducted following the manufacturer s protocol

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Statistical analysis was performed with the statistical software program R (ver. 2.7.2, 3.1.2). The CEL files were normalized using the DFW method (R ver. 2.7.2), and PCA was performed using R ver. 3.1.2. Using the Rank Products method (R ver. 3.1.2), probe sets that met the criterion of FDR < 0.05 were extracted as DEGs. Canonical pathway analysis of the DEGs was performed with Qiagen s Ingenuity Pathway Analysis (IPA, www.qiagen.com/ingenuity) (Qiagen). Pathways with p-value < 0.05 and |Z-score| 2 were extracted as being significantly regulated.

label: biotin

source_name: Human vascular smooth muscle cell

label_protocol: Biotin-labeled cRNA was synthesized using a Genechip 3 IVT PLUS Reagent Kit (Thermo Fisher Scientific)

growth_protocol: Human aortic smooth muscle cells (HASMCs, ATCC) were grown in Smooth Muscle Cell Medium containing apo-transferrin, insulin, fibroblast growth factor-2, insulin-like growth factor-1, hydrocortisone, and 5% fetal bovine serum.Cells were maintained in a humidified incubator at 37 °C with 5% CO2.

extract_protocol: total RNA was purified with the RNeasy Mini Kit (Qiagen, Hilden, Germany). The concentration and purity were checked using a NanoDrop-1000 spectrophotometer (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: HASMCs (passages 4-6) were serum deprived for 24 hours to achieve synchronous growth, following which the cells were exposed to 5-mM D-glucose (normal control, NC), 33mM D-glucose + 5-μM PARP1 inhibitor PJ34 (HG+PJ34) for 72 hours.

value: High glucose + PARP-1 inhibitor PJ34


title: 24hpi_2_miRNA

description: miRNA.TPM.xls


title: Mock_1_circRNA

description: circRNA.TPM.xlsx


title: Mock_2_circRNA

description: circRNA.TPM.xlsx


title: WT 3

city: Cincinnati

first: Yi

last: Zheng

state: OH

address: 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina RTA2.5 software used for basecalling.
Reads were mapped to mm10 whole genome by using Bowtie2. Aligned reads were processed using Cufflinks and Cuffdiff with the default command options.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Sorted CD31+ tdT+ cells

extract_protocol:
Bone marrows were harvested and CD31+ tdT+ cells were sorted by FACS. RNA was collected using a Qiagen kit with Qiazol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Adult mice were injected with tamoxifen on 4 consecutive days.

value: Bone marrow endothelial cells

value: WT


title: KRasG12D 3


title: WT 4


title: KRasG12D 4


title: 24hpi_1_miRNA

description: miRNA.TPM.xls


title: 24hpi_3_miRNA

description: miRNA.TPM.xls


title: WT 1


title: 6hpi_2_miRNA

description: miRNA.TPM.xls


title: 6hpi_3_miRNA

description: miRNA.TPM.xls


title: WT 2


title: High glucose

description: High glucose

value: High glucose with  PBS


title: KRasG12D 2


title: shARID1A-3

first: Qingyu

last: Luo

address: Panjiayuannanli No.17#, Chaoyang District

department: State Key Laboratory of Molecular Oncology

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
RNA-seq libraries were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina (New England Biolabs, MA, USA) and validated using the 2100 Bioanalyzer (Agilent Technologies).
Libraries were sequenced on a NovaSeq 6000 sequencer (Illumina, CA, USA).
After removing low-quality reads, clean reads were aligned to the human (hg37) genomes using HISAT2 (version 2.0.5).
Differential expression between ARID1A-depleted and control A431 cells was computed using the FPKM cultured by featureCounts (Version 1.5.0-p1).
Genome_build: hg37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: A431 cells

growth_protocol: Cells were cultured in DMEM medium supplemented with 10% FBS

extract_protocol:
Total RNA was isolated from cells using TRIzol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human SCC cell

tag: shRNA


title: 6hpi_1_miRNA

description: miRNA.TPM.xls


title: shARID1A-2


title: Mock_3_miRNA

description: miRNA.TPM.xls


title: KRasG12D 1


title: Mock_1_miRNA

description: miRNA.TPM.xls


title: shARID1A-1


title: 24hpi_3_mRNA

description: mRNA.FPKM.xls


title: shCONTROL-3

value: shcontrol


title: shCONTROL-2


title: 24hpi_1_mRNA

description: mRNA.FPKM.xls


title: 6hpi_3_mRNA

description: mRNA.FPKM.xls


title: shARI-3

data_processing:
RNA-seq libraries were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina (New England Biolabs, MA, USA) and validated using the 2100 Bioanalyzer (Agilent Technologies).
Libraries were sequenced on a NovaSeq 6000 sequencer (Illumina, CA, USA).
After removing low-quality reads, clean reads were aligned to the human (hg37) genomes using HISAT2 (version 2.0.5).
Differential expression between PTL-treated and DMSO-treated cells was computed using the FPKM cultured by featureCounts (Version 1.5.0-p1).
Genome_build: hg37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: KYSE410 cells

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% FBS

value: Human ESCC cell


title: shCONTROL-1


title: 24hpi_2_mRNA

description: mRNA.FPKM.xls


title: shARI-2


title: shU11-2


title: Mock_3_mRNA

description: mRNA.FPKM.xls


title: shARI-1


title: Mock_2_mRNA

description: mRNA.FPKM.xls


title: shU11-1


title: shU11-3


title: Mock_2_miRNA

description: miRNA.TPM.xls


title: shc-1


title: 6hpi_2_mRNA

description: mRNA.FPKM.xls


title: Mock_1_mRNA

description: mRNA.FPKM.xls


title: shc-2


title: A.pp 4074 NarP DAP-Seq control

city: Wuhan

first: Lu

last: Li

email: sakura.tree@163.com, xuzf@mail.hzau.edu.cn, xuzhuofei@sohu.com, kobe2071@tom.com

state: Hubei

address: Shizishan Street 1

institute: Huazhong Agricultural University

description: The  control which contains only sheared genomic DNA.

data_processing:
Library strategy: DAP-seq
A total of 1022667 reads after trimming were aligned to the genome of the A. pleuropneumoniae 4074 strain using Bowtie2
Then it was analyzed using MACS2 (version 1.4.2 20120305)  with defaulted settings to call peaks.
Potential promoter regions (upstream regions of any ORFs) fell in the peaks were taken as the potential targets that NarP bound.
Genome_build: ASM17849v1 [ADOD00000000.1]
Supplementary_files_format_and_content: bed format, it  contains the locations for every peak, and the summit height of fragment pileup.

organism: Actinobacillus pleuropneumoniae

source_name: Actinobacillus pleuropneumoniae 4074 cells

growth_protocol: A. pleuropneumoniae (strain  4074) was cultured at 37 °C in Tryptic Soy Broth (TSB) or on Tryptic Soy Agar plates (TSA, ) supplemented with NAD at 10 mg/ml.

extract_protocol:
The genomic DNA of A. pleuropneumoniae was prepared using a DNeasy Blood & Tissue Kit (Qiagen).
1 μg genomic DNA was sheared to an average length of 300-500 bp by ultra-sonication for 16 min at 20% amplitude with 2 seconds on and 8 seconds off on ice. The size of the sheared genomic DNA was checked using 1 % agarose gel. The sheared DNA fragments were treated with Klenow enzyme to generate blunt ends, phosphorylated and 3’-end adenylated followed by ligation with paired-end adapters. The fragments with adapters on both ends were enriched by a ten-cycle PCR and purified using a QIAquick PCR Purification Kit. The adapter-containing DNA fragments were then subject to DNA affinity purification. Briefly, the DNA fragments were mixed with the purified his-tagged NarP in the reaction buffer (10 mM Tris HCl, pH 7.5, 1 mM DTT, 5 mM MgCl2, 50 mM acetyl phosphate and 25% glycerol) in which acetyl phosphate was used to activate NarP. The mixture was incubated at 25 °C for 30 minutes and then incubated with 30 μl of Ni-NTA resin that had been equilibrated in binding buffer 2 (10 mM Tris-HCl, pH 7.5, 5 mM MgCl2, 50 mM KCl, and 25% glycerol) for 30 min. The resin was washed three times with binding buffer 2 and the protein was eluted with elution buffer (20 mM sodium phosphate buffer pH 8, 500 mM NaCl, and 500 mM imidazole). The DNA bound to NarP was recycled using a Qiaquick PCR purification kit.


title: A.pp 4074 NarP DAP-Seq

description: The sheared genomic DNA bound with activated NarP.


title: ChIP-seq of WCE [input-RNAPIIser2P]

status: Public on Nov 29 2019

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

description:
Sample grown at 32°C, crosslinking performed using 1% formaldehyde for 20 min at room temperature, whole-cell extract, sequenced on MiSeq platform
RNAPII_Ser2P_Input

data_processing:
Alignment of adapter-trimmed reads were done using BWA-MEM.
For H3K9me ChIP-seq, reads per Genomic Content (RPGC) values were obtained using Deeptools suite. Correction for GC bias was assessed using input and the parameter--effectiveGenomeSize 12611000 in the correctGCbias module. Coverage was computed using the bamCoverage module and parameters --effectiveGenomeSize 12611000 --normalizeUsing RPGC --smoothLength 10 --binSize 1. Module bamCompare was used to compute input normalized enrichment values. For all other ChIP-seq coverage data, trimmed reads were aligned with BWA to the S. pombe v2.29 reference genome with defaults and the “-M” option for compatibility with Picard tools to produce BAM files. Aligned reads were deduplicated using Picard tools and used for normalization to reads per million (RPM) mapped. Normalized samples were then subject to input normalization by input subtraction from the immunoprecipitation sample. Bedtools was used to produce normalized coverage plot bedgraph files. Fold-enrichment bedgraphs were generated using MACS2.
Enrichment values are calculated for IP relative to whole-cell extract input control
For peak-calling, adapter-trimmed reads were aligned using STAR and normalized to reads per million (RPM). The locations of Dhp1 or Iss1-specific peaks were determined from normalized BedGraphs by identifying peaks in both the ChIP and input samples using an in-house script. Peaks that were found in both the ChIP and input BedGraphs were removed and the positions of the novel peaks that remained, those found only in the ChIP BedGraphs, were deemed to be Dhp1 or Iss1-specific.
Genome_build: asm294v2.29
Supplementary_files_format_and_content: bigWig and Bedgraph

organism: Schizosaccharomyces pombe

source_name: log. growing cells

growth_protocol: Cultures were grown to logarithmic growth phase in rich media (YEA) at 18°C or 32°C.

extract_protocol:
Cells were fixed with 1% formaldehyde at room temperature for 20 minutes. Additional crosslinking with DMA were performed as needed for in each sample as indicated in each description section. Cells were lysed using bead-beater method. Lysates were sonicated and immunoprecipitations were performed in cold room conditions. Whole-cell extracts (WCE) were used as input control for each ChIP experiment. Reverse crosslinking was performed overnight at 65˚C, followed by treatment with RNase A and proteinase K. DNA was purified using QIAquick PCR purification kit (cat. no. 28014).
NEBNext Ultra II DNA Library Prep kit (NEB, E7645S) was used according to manufacturer's recommendation.
Libraries were analyzed using an Agilent 2100 BioAnalyzer (Agilent) and sequenced on the Illumina MiSeq or NextSeq 500 platform.

treatment_protocol: Genomic deletions of indicated genes in non-wild-type cells. Genomic C-terminal tagging with GFP of genes where indicated.

value: WCE, WT cells


title: ChIP-seq of RNA Pol II serine-2P in mmi1∆ cells

description:
Sample grown at 32°C, crosslinking performed using 1% formaldehyde for 20 min at room temperature, ChIP was performed using anti-Pol II ser2P (ab5095) and was sequenced on MiSeq platform
RNAPII_Ser2P_mmi1∆

value: mmi1delta cells


title: ChIP-seq of WCE [Iss1GFP_input]

description:
Sample grown at 32°C, additional crosslinking was performed with DMA for 45 minutes at room temperature in addition to formaldehyde, whole-cell extract, sequenced on MiSeq platform
Iss1-GFP_Input

value: WCE WT cells


title: ChIP-seq of RNA Pol II serine-2P in WT cells

description:
Sample grown at 32°C, crosslinking performed using 1% formaldehyde for 20 min at room temperature, ChIP was performed using anti-Pol II ser2P (ab5095) and was sequenced on MiSeq platform
RNAPII_Ser2P_WT

value: wild type cells


title: ChIP-seq of RNA Pol II serine-2P in ssu72∆ cells

description:
Sample grown at 32°C, crosslinking performed using 1% formaldehyde for 20 min at room temperature, ChIP was performed using anti-Pol II ser2P (ab5095) and was sequenced on MiSeq platform
RNAPII_Ser2P_ssu72∆

value: ssu72delta cells


title: 6hpi_1_mRNA

description: mRNA.FPKM.xls

value: lung adenocarcinoma

value: Calu-3 cells

value: MERS-CoV at 4 MOI


title: RNA-seq Control rep 1

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

data_processing:
Reads were aligned using danRer7 as reference genome and Tophat2 software. Duplicated reads were removed with Picard tool.
Differential gene expression analysis: Control and SU5402 treatment conditions were compared with Cuffdiff program from Cufflinks software package.
Genome_build: danRer7 (Zv9)

organism: Danio rerio

source_name: whole embryo

growth_protocol: Embryos were raised at 28ºC untill they reached the desired developmental stage. They were dechorionated with pronase before fixation.

extract_protocol:
Total RNA was isolated at the dome stage using Trizol.
Primers with Illumina adaptors were used to amplify the library. Different samples were multiplexed for sequencing.

treatment_protocol: FGF receptor inhibitor SU5402 was dissolved in demethylsulphoxide (DMSO) at a concentration of 40mM, and added to the embryo medium at a final concentration of 20 µM when embryos were at 2 cells stage. Control embryos were incubated with the same volume of DMSO during the same period.

value: whole embryo

tag: developmental stage

value: dome


title: ATAC-seq Control rep 1

data_processing:
Alignment: reads were aligned using danRer7 as reference genome and Bowtie2 software.
Filtering duplicates: duplicated pairs were removed using Samtools software.
Localization of the cleavage site: the enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions.
Visualization: bigWig files were visualized using local browser
Genome_build: danRer7 (Zv9)


title: ChIP-seq of RNA Pol II serine-2P in swd22∆ cells

description:
Sample grown at 32°C, crosslinking performed using 1% formaldehyde for 20 min at room temperature, ChIP was performed using anti-Pol II ser2P (ab5095) and was sequenced on MiSeq platform
RNAPII_Ser2P_swd22∆

value: swd22delta cells


title: ChIP-seq of Iss1-GFP mmi1∆ cells

description:
Sample grown at 32°C, additional crosslinking was performed with DMA for 45 minutes at room temperature in addition to formaldehyde, ChIP was performed using anti-GFP (ab290) and was sequenced on MiSeq platform
Iss1-GFP_mmi1∆ IP

value: Iss1-GFP in mmi1delta cells


title: ChIP-seq of Iss1-GFP WT cells

description:
Sample grown at 32°C, additional crosslinking was performed with DMA for 45 minutes at room temperature in addition to formaldehyde, ChIP was performed using anti-GFP (ab290) and was sequenced on MiSeq platform
Iss1-GFP_WT IP

value: Iss1-GFP in WT cells


title: shc-3


title: RNA-seq SU5402 rep 2


title: ATAC-seq Control rep 2


title: LIB030929_GEN00110966_S119

city: Boston

first: Pierce

last: Ogden

state: MA

address: 3 Blackfan Circle, CLSB 528/4C

institute: Harvard

description: AAV genomes extracted from mouse tissues

data_processing:
Library strategy: amplicon seq
for all samples, we use python to process fastqs and counted the  barcodes
the counted barcodes are then merged onto a table containing the allele information for each barcode using python scripts
Genome_build: AAV2
Supplementary_files_format_and_content: barcode abundances and associated mutation information

organism: Adeno-associated virus

source_name: Mouse tissue (Liver) - AAV Genome Multi-mutants

extract_protocol:
AAV were isolated according to methods described in paper
libraries were prepared using illumina sequencing primers

tag: experiment

value: Tissue tropism experiment

value: viral DNA


title: RNA-seq SU5402 rep 1


title: ATAC-seq SU5402 rep 1


title: LIB030929_GEN00110871_S24


title: LIB030929_GEN00110969_S122


title: LIB030929_GEN00110967_S120


title: ATAC-seq SU5402 rep 2


title: LIB030929_GEN00110968_S121


title: LIB030929_GEN00110869_S22


title: LIB030929_GEN00110857_S10


title: LIB030929_GEN00110868_S21


title: LIB030929_GEN00110867_S20


title: LIB030929_GEN00110870_S23


title: LIB030929_GEN00110855_S8


title: LIB030929_GEN00110856_S9


title: LIB030929_GEN00110854_S7


title: LIB029294_GEN00100249_S42

description: Plasmids produced through cloning in E.coli

source_name: DNA plasmid - multi-mutants

value: capsid production

value: plasmid DNA


title: RNA-seq Control rep 2


title: LIB029294_GEN00100237_S30


title: LIB029294_GEN00100243_S36


title: packaging_MAAP_pRep-only_complement_rep_2

description: AAV packaging complemented with MAAP

source_name: AAV Capsid - MAAP complementation

value: MAAP complementation assay

value: AAV genome DNA


title: packaging_MAAP_pRep-only_complement_rep_1

description: AAV packaging complemented with MAAP


title: packaging_MAAP_P27_CCC_complement_rep_2

description: AAV packaging complemented with MAAP


title: packaging_MAAP_WT_complement_rep_2

description: AAV packaging complemented with MAAP


title: antibody_A20_AAV_rep_1

description: AAV capsid neutralized with A230 antibody then infection tested

source_name: AAV Capsid - anitbody neutrilization

value: antibody neutrilization assay


title: thermo_virus_Rep2_temp_90C_rep_1

description: AAV capsid heated and digested to determine thermostability

source_name: AAV Capsid - thermostability experiement

value: capsid thermostability screen


title: thermo_virus_Rep2_temp_85C_rep_1


title: thermo_virus_Rep2_temp_85C_rep_2


title: thermo_virus_Rep2_temp_80C_rep_2


title: thermo_virus_Rep2_temp_70C_rep_2


title: LIB029294_GEN00100255_S48


title: thermo_virus_Rep2_temp_80C_rep_1


title: thermo_virus_Rep2_temp_75C_rep_1


title: thermo_virus_Rep2_temp_70C_rep_1


title: thermo_virus_Rep2_temp_69C_rep_2


title: thermo_virus_Rep2_temp_68C_rep_2


title: packaging_MAAP_P32_ATA_complement_rep_1

description: AAV packaging complemented with MAAP


title: thermo_virus_Rep2_temp_66C_rep_2


title: thermo_virus_Rep2_temp_67C_rep_1


title: thermo_virus_Rep2_temp_69C_rep_1


title: thermo_virus_Rep2_temp_65C_rep_1


title: packaging_MAAP_P32_ATA_complement_rep_2

description: AAV packaging complemented with MAAP


title: packaging_MAAP_WT_complement_rep_1

description: AAV packaging complemented with MAAP


title: packaging_MAAP_P27_CCC_complement_rep_1

description: AAV packaging complemented with MAAP


title: thermo_virus_Rep2_temp_60C_rep_2


title: antibody_A20_AAV_rep_2


title: thermo_virus_Rep2_temp_55C_rep_2


title: thermo_virus_Rep2_temp_90C_rep_2


title: thermo_virus_Rep2_temp_75C_rep_2


title: thermo_virus_Rep2_temp_68C_rep_1


title: thermo_virus_Rep2_temp_55C_rep_1


title: thermo_virus_CMV2_temp_90C_rep_2


title: thermo_virus_CMV2_temp_85C_rep_1


title: thermo_virus_CMV2_temp_80C_rep_2


title: thermo_virus_CMV2_temp_75C_rep_1


title: thermo_virus_CMV2_temp_80C_rep_1


title: thermo_virus_Rep2_temp_67C_rep_2


title: thermo_virus_CMV2_temp_70C_rep_1


title: thermo_virus_Rep2_temp_65C_rep_2


title: thermo_virus_Rep2_temp_66C_rep_1


title: thermo_virus_CMV2_temp_70C_rep_2


title: thermo_virus_CMV2_temp_68C_rep_2


title: thermo_virus_CMV2_temp_68C_rep_1


title: thermo_virus_CMV2_temp_67C_rep_2


title: thermo_virus_CMV2_temp_69C_rep_1


title: thermo_virus_CMV2_temp_67C_rep_1


title: thermo_virus_Rep2_temp_60C_rep_1


title: thermo_virus_CMV2_temp_65C_rep_2


title: thermo_virus_CMV2_temp_85C_rep_2


title: thermo_virus_CMV2_temp_66C_rep_1


title: thermo_virus_CMV2_temp_60C_rep_1


title: thermo_virus_CMV2_temp_60C_rep_2


title: thermo_virus_CMV2_temp_55C_rep_2


title: thermo_virus_CMV2_temp_55C_rep_1


title: thermo_virus_CMV2_temp_90C_rep_1


title: thermo_virus_CMV2_temp_75C_rep_2


title: lung_mouse_2_virus_2_techrep_4

source_name: Mouse tissue - AAV Genome

value: tissue tropism screen


title: lung_mouse_2_virus_2_techrep_3


title: thermo_virus_CMV2_temp_66C_rep_2


title: lung_mouse_2_virus_2_techrep_1


title: thermo_virus_CMV2_temp_69C_rep_2


title: lung_mouse_2_virus_2_techrep_2


title: lung_mouse_2_virus_2_techrep_0


title: lung_mouse_1_virus_2_techrep_3


title: Wt25_5hmCIP_Rep3

city: Singapore

first: Swarnaseetha

last: Adusumalli

address: 1 Research Link,  National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

description:
Wt25_5hmCIP_Rep3
5MEDIP-seq

data_processing:
5MEDIP-seq data processing: Multiple mapped reads were marked and filtered out using the Picard MarkDuplicates. Bigwigs were generated using bamCoverage from DeepTools. Differential 5-hydroxymethylated regions (DhMRs) between wild-type (Wt25) and phosphor-mutant (AA10) TET3 mESCs were determined from the uniquely aligned reads using MEDIPS (.bed files).
Genome_build: GRCm38.87
Supplementary_files_format_and_content: bigwigs, RNA-seq-differetially expressed genes (xlsx), 5hmC-differential hydroxymethylated regions (bed)

source_name: mESC

growth_protocol: Tet1, 2 and 3 triple knockout (TKO) mouse embryonic stems (mESC) of mixed C57BL/6J-129V backgrounds (Hu et al., 2014) was cultured in 2i media composed of DMEM GlutaMax 1 mM PD0325901 (StemGent), and 3 mM CHIR99021 (Axon Medchem), 1000 U/ml murine leukemia inhibitory factor (LIF, Chemicon), and 1 × penicillin/streptomycin (PS, Gibco-BRL).

extract_protocol:
Genomic DNA isolated by overnight lysis (100 mM Tris-HCl pH8.0, 200mM NaCl, 10mM EDTA, 0.5% SDS, 50 μg proteinase K) and phenol/chloroform extraction was fragmented to 200-400 bp using Covaris M220 (PIP50, Duty 20%, cycles/burst 200, Time 200 sec). 5 μg of DNA fragments was then subjected to end repair (NEB E6050), A-tailing (NEB M0212L) and adaptor ligation (NEB M0202M). Adaptor-ligated DNA was denatured by boiling for 10 min. 0.4 μg of DNA was set aside as input while 4 μg of DNA was diluted to 500 μl in IP buffer (final concentration of 10 mM Na phosphate pH 7.0, 140 mM NaCl, 0.05% Triton) and incubated overnight with 5 μg of anti-5hmC antibody (Active motif 39791) at 4◦C. On the following day, 30 μl of pre-blocked (0.5% BSA in PBS) Protein G Dynabeads (Life Technologies 10003D) was added to the DNA-antibody complex. After incubating for 2 hr at 4◦C, Dynabeads was captured on magnetic stand and washed 4 times with IP buffer. IP DNA was eluted from Dynabeads with 500 μl of digestion buffer (50 mM Tris pH8.0, 10 mM EDTA, 0.5% SDS, 100 μg of proteinase K) for 4 hrs at 55◦C. Input and IP DNA was purified by phenol/chloroform and ethanol precipitation.
Barcoded libraries was then generated by KAPA real-time library amplification kit (KK2701). PCR libraries between 200-500bp were excised from DNA gel and purified with QIAGEN gel extraction kit.

treatment_protocol: Tet1, 2 and 3 TKO mESC was infected with lentiviral plasmids containing wild-type (WT) or phosphor-mutant (AA) using Lenti-X packaging single shots protocol (Clontech). WT25 and AA10 lines were single ESC clone selected by puromycin (0.1ug/ml) and expressed similar level of Tet3 protein.

value: embryonic stem cells stage

tag: background strain

value: mixed C57BL/6J-129V background

tag: transfected with

value: wild type Tet3


title: lung_mouse_1_virus_2_techrep_2


title: lung_mouse_1_virus_2_techrep_0


title: Mm-Uninf-AB1116

first: Timothy

middle: G

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

data_processing:
Illumina RTA 2.4.6  and bcl2fastq 2.17 for fastq generation
Quality trim and alignment using CLC genomics workbench (Aug 2015)
Alignment was initially to the Py genome, all unaligned reads were then aligned to Mm genome.
expression defined as total of exon-mapped reads per gene (reads with more than 10 equivalent alignments were ignored)
upper quartile normalization of inflated log2 read count
Genome_build: GRCm38, PyoeliiyoeliiYM (plasmoDB release 24)
Supplementary_files_format_and_content: Tabular (excel worksheet) formatted read count per gene (total reads mapped to gene exons) "ge_count_20150812-yaox4-20150810-D1_high_stringency.xlsx"

molecule: polyA RNA

source_name: Mouse red blood cells

growth_protocol: Inbred female C57BL/6 mice, aged 6–8 weeks old

extract_protocol:
The obtaining pellet will be suspended in 5ml QIAzol Lysis Reagent (QIAGEN) and stored in -80®C immediately. Total RNA will be extracted using the Direct-zol™ RNA MiniPrep (Zymoresearch) following the manufacturer's protocol
Illumina Tru-seq stranded mRNA

treatment_protocol: Parasites will be thawed from frozen stocks and injected into naïve C57BL/6 mice to initiate infection. When the parasitemia reaches 20%-30%, blood with be harvested by cardiac puncture or from tail. An inoculum containing 1 × 106 infected red blood cells (iRBCs) suspended in 100 μL PBS, pH 7.4, from the donor mice will be injected i.v. into experimental mice (n=3  mice per clone or strain). . Then, four days post-infection, the experimental mice will be anesthetized and blood will be withdrawn by cardiac puncture (terminal bleeding) and directly transferred to anticoagulant (0.9% NaCl, 1.5 Na-Citrate, 10ml). The cell pellet will be collected by centrifugation at 2500rpm for 5min at room temperature, followed by RBC lysis with 5ml ACK Lysing Buffer (life technologies) on ice for 5min.  Afterwards, 5ml PBS will be added and centrifuged at 2500rpm for 5min at room temperature.

value: red blood cells

tag: strain

tag: age

value: 6-8 weeks old

tag: Sex

value: female

tag: agent

value: Plasmodium yoelii

tag: py strain

value: naive


title: Mm-N67/YtoC-AB1253

tag: cell type

value: N67 YtoC

tag: dpi


title: AA10_5hmCIP_Rep3

description:
AA10_5hmCIP_Rep3
5MEDIP-seq

value: phosphor mutant Tet3 (AA10)


title: Mm-Uninf-AB1257


title: lung_mouse_2_virus_1_techrep_2

tag: tissue


title: AA10_gDNA_5hmc_Rep3

description:
AA10_gDNA_5hmc_Rep3
5MEDIP-seq


title: thermo_virus_CMV2_temp_65C_rep_1


title: Mm-Unif-AB1095


title: lung_mouse_2_virus_1_techrep_1


title: lung_mouse_2_virus_1_techrep_0


title: Mm-N67C/CtoC-AB1093

value: N67C/ CtoC


title: lung_mouse_1_virus_1_techrep_2


title: Wt25_gDNA_5hmc_Rep1

description:
WT25 gDNA input Rep1
5MEDIP-seq

data_processing:
Raw sequencing reads was assessed using FastQC and mapped to the Ensembl mouse genome using STAR.   RNA-seq data processing:Read counts were generated using featureCounts and differential expression analysis between WT and AA Tet3 was performed using DESeq2. The relative expression level of all genes was determined by Cufflinks.  H3K27ac-ChIP-seq  data processing: Multiple mapped reads were marked and filtered out using the Picard MarkDuplicates. H3K27ac enriched peaks were identified using Homer findpeaks.   5MEDIP-seq data processing: Multiple mapped reads were marked and filtered out using the Picard MarkDuplicates. Differential 5-hydroxymethylated regions (DhMRs) between wild-type (Wt25) and phosphor-mutant (AA10) TET3 mESCs were determined from the uniquely aligned reads using MEDIPS.
Genome_build: GRCm38.87
Supplementary_files_format_and_content: bigwigs, RNA-seq-differetially expressed genes (xlsx), 5hmC-differential hydroxymethylated regions (bed)

extract_protocol:
5MEDIP-seq: Genomic DNA isolated by overnight lysis (100 mM Tris-HCl pH8.0, 200mM NaCl, 10mM EDTA, 0.5% SDS, 50 μg proteinase K) and phenol/chloroform extraction was fragmented to 200-400 bp using Covaris M220 (PIP50, Duty 20%, cycles/burst 200, Time 200 sec). 5 μg of DNA fragments was then subjected to end repair (NEB E6050), A-tailing (NEB M0212L) and adaptor ligation (NEB M0202M). Adaptor-ligated DNA was denatured by boiling for 10 min. 0.4 μg of DNA was set aside as input while 4 μg of DNA was diluted to 500 μl in IP buffer (final concentration of 10 mM Na phosphate pH 7.0, 140 mM NaCl, 0.05% Triton) and incubated overnight with 5 μg of anti-5hmC antibody (Active motif 39791) at 4◦C. On the following day, 30 μl of pre-blocked (0.5% BSA in PBS) Protein G Dynabeads (Life Technologies 10003D) was added to the DNA-antibody complex. After incubating for 2 hr at 4◦C, Dynabeads was captured on magnetic stand and washed 4 times with IP buffer. IP DNA was eluted from Dynabeads with 500 μl of digestion buffer (50 mM Tris pH8.0, 10 mM EDTA, 0.5% SDS, 100 μg of proteinase K) for 4 hrs at 55◦C. Input and IP DNA was purified by phenol/chloroform and ethanol precipitation.
Genomic DNA isolated by overnight lysis (100 mM Tris-HCl pH8.0, 200mM NaCl, 10mM EDTA, 0.5% SDS, 50 μg proteinase K) and phenol/chloroform extraction was fragmented to 200-400 bp using Covaris M220 (PIP50, Duty 20%, cycles/burst 200, Time 200 sec). 5 μg of DNA fragments was then subjected to end repair (NEB E6050), A-tailing (NEB M0212L) and adaptor ligation (NEB M0202M). Adaptor-ligated DNA was denatured by boiling for 10 min. 0.4 μg of DNA was set aside as input while 4 μg of DNA was diluted to 500 μl in IP buffer (final concentration of 10 mM Na phosphate pH 7.0, 140 mM NaCl, 0.05% Triton) and incubated overnight with 5 μg of anti-5hmC antibody (Active motif 39791) at 4◦C. On the following day, 30 μl of pre-blocked (0.5% BSA in PBS) Protein G Dynabeads (Life Technologies 10003D) was added to the DNA-antibody complex. After incubating for 2 hr at 4◦C, Dynabeads was captured on magnetic stand and washed 4 times with IP buffer. IP DNA was eluted from Dynabeads with 500 μl of digestion buffer (50 mM Tris pH8.0, 10 mM EDTA, 0.5% SDS, 100 μg of proteinase K) for 4 hrs at 55◦C. Input and IP DNA was purified by phenol/chloroform and ethanol precipitation.


title: Mm-N67/YtoY-AB1091

value: N67/ YtoY


title: lung_mouse_1_virus_1_techrep_1


title: lung_mouse_1_virus_1_techrep_0


title: Wt25_gDNA_5hmc_Rep2

description:
WT25 gDNA input Rep2
5MEDIP-seq


title: kidney_mouse_2_virus_2_techrep_4


title: Wt25_gDNA_5hmc_Rep3

description:
Wt25_gDNA_5hmc_Rep3
5MEDIP-seq


title: Wt25_5hmCIP_Rep2

description:
WT25 5hmC DNA-IP Rep2
5MEDIP-seq


title: kidney_mouse_2_virus_2_techrep_3


title: Mm-N67C/CtoY-AB1088

value: N67C/ CtoY


title: Mm-N67/YtoC-AB1085

value: N67/ YtoC


title: kidney_mouse_2_virus_2_techrep_2

value: AAV genome DNA


title: lung_mouse_2_virus_1_techrep_3


title: AA10_gDNA_5hmc_Rep1

description:
AA10 gDNA input Rep1
5MEDIP-seq


title: Wt25_5hmCIP_Rep1

description:
WT25 5hmC DNA-IP Rep1
5MEDIP-seq


title: kidney_mouse_1_virus_2_techrep_4


title: kidney_mouse_1_virus_2_techrep_3


title: kidney_mouse_1_virus_2_techrep_2


title: Mm-N67/YtoC-AB1083


title: Mm-N67C-AB1081


title: kidney_mouse_1_virus_2_techrep_1


title: AA10_5hmCIP_Rep2

description:
AA10 5hmC DNA-IP Rep2
5MEDIP-seq


title: AA10_gDNA_5hmc_Rep2

description:
AA10 gDNA input Rep2
5MEDIP-seq


title: lung_mouse_1_virus_2_techrep_1


title: kidney_mouse_1_virus_2_techrep_0


title: AA10_5hmCIP_Rep1

description:
AA10 5hmC DNA-IP Rep1
5MEDIP-seq


title: kidney_mouse_2_virus_1_techrep_4


title: kidney_mouse_2_virus_1_techrep_3


title: kidney_mouse_2_virus_1_techrep_2


title: kidney_mouse_2_virus_1_techrep_1


title: SH-SY5Y cells, Input-1

city: Cambridge

first: Christine

middle: E

last: Holt

address: Anatomy Bldg., Downing St.

department: Department of PDN

country: United Kingdom

institute: University of Cambridge

data_processing:
Illumina bcl2fastq2 Conversion Software v2.20 was used for de-multiplexing and base-calling.
Sequence reads were aligned to the genome using Hisat2 v2.1.0
Read counts for each gene were determined using HTSeq version 0.11.0.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts for each gene

source_name: SH-SY5Y cells

growth_protocol: The cells were cultured at 37C and 5% CO2 in DMEM high glucose medium supplemented with 10% FBS

extract_protocol:
The lysate of SH-SY5Y cells was incubated with magnetic Dynabeads pre-coupled with antibodies (mouse-anti-DCC (BD Biosciences, 554223); rabbit-anti-Nrp1 (Abcam, ab81321)) for 1.5 hours at 4°C. Beads were then washed 3 times and processed for RNA isolation.
Immunopurified RNAs are reverse-transcribed, and then amplified by a PCR-based method (Tang et al., Nat Methods 6, 2009).

tag: cell line

value: neuroblastoma cells

tag: rip antibody

value: Input


title: kidney_mouse_2_virus_2_techrep_1

value: tissue tropism screen


title: SH-SY5Y cells, Input-3


title: SH-SY5Y cells, Input-2


title: kidney_mouse_1_virus_1_techrep_4


title: kidney_mouse_2_virus_2_techrep_0


title: AA10_mRNA_Rep2

description:
AA10 RNA-seq Rep2
DEG.xlsx

extract_protocol:
RNA-seq: Total RNA was isolated from approximately 2 million WT25 and AA10 Tet3 mESCs with RNAzol®RT (Sigma) according to manufacturer protocol. Total RNA samples from biological replicates were sent to BGI (Hong Kong) for high-throughput sequencing according to company’s protocol. RNA quality was assessed with Agilent 2100 bioanalyzer.
Following DNAse I treatment, mRNA enriched by magnetic beads coupled to Oligo-dT was fragmented and used as template for cDNA library construction. Short DNA fragments were then subjected to end-repair, A-tailing, adaptor ligation, size selection and sequenced on Illumina HiSeqTM4000.

value: embryonic stem cells stage

value: mixed C57BL/6J-129V background


title: SH-SY5Y cells, Nrp1-IP-3

value: rabbit-anti-Nrp1 (Abcam, ab81321)


title: kidney_mouse_1_virus_1_techrep_1


title: SH-SY5Y cells, Nrp1-IP-2


title: AA10_mRNA_Rep1

description:
AA10 RNA-seq Rep1
DEG.xlsx


title: heart_mouse_4_virus_2_techrep_2


title: Wt25_MNase_Rep2

description: WT25 MNase treated input Rep2

extract_protocol:
H3K27ac-ChIP-seq: Cell pellet (2x106) was resuspended in 400 μl of NBA buffer (85 mM NaCl, 5.5% sucrose, 10 mM Tris-HCl, pH 7.5, 0.2 mM EDTA, 0.2 mM PMSF, 1 mM DTT, 5mM sodium butyrate and 1× protease inhibitors, Roche) followed by equal volume of 0.1% NP-40 in NBA buffer. After 5 min of incubation on ice, nuclei were pelleted at 4,000g for 3 min at 4°C. The nuclear pellet was washed with 1 ml of NBR buffer (85 mM NaCl, 5.5% sucrose, 10 mM Tris-HCl, pH 7.5, 3 mM MgCl2, 1.5 mM CaCl2, 0.2 mM PMSF, 1 mM DTT, 5mM sodium butyrate and 1× protease inhibitors), pelleted and resuspended in 750 μl of NBR buffer (20 μg of RNase A). After 5 min incubation at 20°C for 5 min, chromatin was cut with micrococcal nuclease at 37°C for 15 min (Worthington, titrated to give 75% mononucleosomes: 25% dinucleosomes). Digestion was stopped with the addition of equal volume of STOP buffer (215 mM NaCl, 10 mM Tris-HCl, pH 8, 20 mM EDTA, 5.5% sucrose, 2% Triton X-100, 0.2 mM PMSF, 1 mM DTT, 5mM sodium butyrate and 1× protease inhibitors). The digested nuclei was sonicated for 10 seconds with ultrasonic processor (Vibra-CellTM VC 130S at output watts of 6) and incubated on ice for 3-4 hours to release soluble chromatin. After centrifugation at 12,000g for 10 min at 4°C, the supernatant was transferred to new eppendorf tube. Ten percent of soluble chromatin was retained as input, and the remainder was incubated with ~5 μg of antibody (H3K27ac, Abcam ab4729) overnight at 4°C on a rotating wheel. 25 μl of Protein A Dynabeads (Life Technologies, 10002D) was washed once and blocked overnight in PBS containing 5 mg/ml BSA and 0.1 mM PMSF. On the next day, the blocking buffer was removed from Dynabeads. The chromatin/antibody mixture was added to Dynabeads and incubated for 4 hours with agitation at 4°C. The immune complexes bound to Dynabeads were washed five times with wash buffer (150 mM NaCl, 10 mM Tris-HCl, pH 8, 2 mM EDTA, 1% NP-40 and 1% sodium deoxycholate) on nutating mixer and once in room-temperature TE buffer for 10 min/wash. Chromatin was released from the Dynabeads by incubation with 0.1 M NaHCO3 in 1% SDS for 30 min at 37°C followed by the addition of proteinase K (100 μg/ml) and Tris, pH 6.8 (100 mM), and overnight incubation at 55°C. 5 M NaCl was added to a final concentration of 0.2 M. DNA was extracted with phenol/chloroform and chloroform, followed by ethanol precipitation.
Equal amount (10-20 ng) of input or ChIP DNA was incubated with NEBNext End repair module (NEB E6050) in a 20 μl reaction at 20°C for 30 min. After Ampure purification, the blunt DNA was subjected to A-tailing with Klenow Fragment (3´→5´exo-) in a 30 μl reaction at 37°C for 30 min. The Ampure purified DNA was then ligated to universal adaptor with T4 ligase (NEB M0202) overnight at 25°C. Amplification of the ligated DNA libraries was carried using barcoded primers and KAPA real-time library amplification kit (KK2701). PCR libraries between 200-500bp were excised from DNA gel and purified with QIAGEN gel extraction kit.

value: wild type Tet3


title: heart_mouse_4_virus_2_techrep_1


title: Mm-N67-AB1079

value: red blood cells

value: 6-8 weeks old

value: female


title: SH-SY5Y cells, Nrp1-IP-1


title: heart_mouse_2_virus_2_techrep_3


title: Wt25_mRNA_Rep1

description:
WT25 RNA-seq Rep1
DEG.xlsx


title: Wt25_MNase_Rep1

description: WT25 MNase treated input Rep1


title: heart_mouse_2_virus_2_techrep_2


title: heart_mouse_2_virus_2_techrep_0


title: Wt25_K27ac_Rep2

description: WT25 H3K27ac ChIP Rep2


title: heart_mouse_2_virus_2_techrep_1


title: SH-SY5Y cells, DCC-IP-2

value: mouse-anti-DCC (BD Biosciences, 554223)


title: SH-SY5Y cells, DCC-IP-3


title: SH-SY5Y cells, DCC-IP-1


title: heart_mouse_1_virus_2_techrep_3


title: heart_mouse_1_virus_2_techrep_2


title: kidney_mouse_1_virus_1_techrep_3


title: Wt25_K27ac_Rep1

description: WT25 H3K27ac ChIP Rep1


title: D14 IRI Unbound-R3

city: St. Louis

first: Monica

last: Chang-Panesso

state: MO

address: 600 S. Euclid Ave CB 8126

department: Medicine / Nephrology

institute: Washington University in St. Louis

data_processing:
RNA-seq reads were aligned to the Ensembl release 76 assembly with STAR version 2.0.4b.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.  Transcript counts were produced by Sailfish version 0.6.3.
Sequencing performance was assessed for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3.
All gene-level and transcript counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Genes or transcripts not expressed in any sample were excluded from further analysis.
Genome_build: Ensembl R76
Supplementary_files_format_and_content: RPKMs

source_name: D14 IRI Unbound, kidney

extract_protocol:
Kidneys were harvested and TRAP performed as previously described (Grgic et al). Briefly, the kidney was homogenized and the homogenate was immunoprecipitated with anti-GFP coated magnetics beads. The RNA bound to the magnetic beads is the “cell-type specific” or “bound” fraction. The “unbound fraction” represents the total kidney. The isolated RNA was purified and RNA integrity was measured with the Agilent Bioanalyzer.
Low Input RNA kit (Takara Bio USA. Mountain View, CA) was used for cDNA library preparation. cDNA libraries and next generation sequencing were performed at the Genome Technology Access Center at Washington University in St. Louis.

treatment_protocol: Bilateral ischemia reperfusion injury (Bi-IRI) was performed in 8-10 week old Kim1GCE; EGFPL10a heterozygous male mice. The mice were anesthesized with isoflurane. Body temperature was maintained between 36.5-37.5 C throughout the surgery. Bilateral flank incisions were made and the kidneys exposed. Ischemia was induced by clamping the renal pedicle with non-traumatic microaneurysm clamps for 20 minutes. After time completion, kidneys were returned to the peritoneal cavity and the peritoneal layer closed with absorbable suture and incisions closed with wound clips. Sham mice underwent the same procedure except for clamping of the renal pedicle. Kidneys were harvested at day 2, 7, and 14. For each time point, there were 3 biological replicates.

value: 8-10 week

value: Mixed background

tag: genotype

value: Kim1-GCE+/-; EGFPL10a+/-

tag: treatment

value: IRI

tag: fraction

value: unbound (represents the total kidney)

tag: time

value: Kidney


title: AA10_MNase_Rep2

description: AA10 MNase treated input Rep2

value: phosphor mutant Tet3 (AA10)


title: D14 IRI Unbound-R2


title: R059-Pano2

city: Stanford

first: Michelle

last: Monje

address: 265 Campus Drive G3035

department: Neurology

institute: Stanford University

data_processing:
Mapping: RNA-seq with tophat2. Default parameters were used against hg19 reference genome
Bed files generated using bedtools bamtobed
bedGraph files were generated using bedtools genomecov, then converted to bigWig using UCSC bedGraphToBigWig
Gene expression: For RNA-seq, gene expression was counted using featureCounts against an RefSeq hg19 GTF without miRNA or snoRNA
Genome_build: hg19

source_name: patient-derived cell culture

growth_protocol: Cells are grown in Tumor Stem Media (TSM), consisting of Neurobasal (-A), DMEM F12, B27 (-A), bFGF, EGF, PDGF-AB, and heparin. See Grasso et al 2015.

extract_protocol:
RNA-seq samples were pelleted and lysed in Trizol reagent then subsequently precipitated and processed through a Zymo RNA Clean and Concentrator-5 column
After extraction from Trizol, RNA-seq samples were poly(A) selected using Dynabeads mRNA Purification Kit (Life Tech) before fragmentation using Thermo AM8740 and Second Strand Synthesis. Libraries were end-repaired using T4 DNA Polymerase, E. coli Klenow fragment, and T4 polynucleotide kinase. DNA was then A-tailed using exo(-) Klenow fragment and ligated to adaptors from NEBNext MultiPlex Oligos using New England BioLabs Quick Ligase.
Libraries were sequenced at 1x75 on an Illumina NextSeq 500

treatment_protocol: Cells were plated at 200k cells/mL and treated with DMSO control, 50nM Panobinostat, 20nM Marizomib, 50nM Panobinostat and 20nM Panobinostat (Combo/Combo Low), or 100nM Panobinostat and 50nM Marizomib (Combo High) for 16 hours

value: Panobinostat


title: heart_mouse_1_virus_2_techrep_1

tag: experiment

value: tissue tropism screen

value: AAV genome DNA


title: R059-Pano1


title: AA10_MNase_Rep1

description: AA10 MNase treated input Rep1

value: embryonic stem cells stage

tag: background strain

value: mixed C57BL/6J-129V background


title: heart_mouse_1_virus_2_techrep_0


title: D14 IRI Unbound-R1


title: AA10_K27ac_Rep2

description: AA10 H3K27ac ChIP Rep2

tag: transfected with


title: D7 IRI Unbound-R3

source_name: D7 IRI Unbound, kidney

tag: strain


title: R059-Mar2

value: Marizomib


title: heart_mouse_4_virus_1_techrep_1


title: heart_mouse_2_virus_1_techrep_1


title: AA10_K27ac_Rep1

description: AA10 H3K27ac ChIP Rep1


title: R059-Mar1


title: D7 IRI Unbound-R1

tag: age


title: D7 IRI Unbound-R2


title: R059-Control2

value: DMSO


title: D2 IRI Unbound-R3

source_name: D2 IRI Unbound, kidney


title: heart_mouse_1_virus_1_techrep_1


title: TGFBR2_M1V_TGF-β1_24h

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

data_processing:
Sequence reads were aligned using STAR aligner with GRCh37 reference genome.
HTSeq-count was used to generate count files.
For each individual, the fold change (FC) between unstimulated and stimulated conditions were calculated. Genes with fold change higher than 1.5 fold in all the controls were used to filter the residual responsive genes to generate heatmaps.
Genome_build: Ensembl GRCh37
Supplementary_files_format_and_content: HTSeq-count is used to get the count files, followed by DESeq2 package in R for normalization and log2 transformation.

source_name: skin fibroblasts

growth_protocol: Skin fibroblasts were cultured in DMEM supplemented with 10% FBS

extract_protocol:
Total RNA was extracted with the RNeasy Plus Micro Kit from QIAGEN
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were left untreated or treated for 2, 6, or 24 hours with IL-17A (100 ng/ml) or TGF-β1 (10 ng/ml)

value: skin fibroblasts

tag: disease state

value: Loeys-Dietz syndrome

value: TGF-β

tag: time point


title: TGFBR2_M1V_TGF-β1_6h


title: TGFBR2_M1V_TGF-β1_2h


title: D2 IRI Unbound-R2

value: 8-10 week


title: R059-Combo2

tag: agent

value: Panobinostat and Marizomib


title: R059-Control1

tag: cell type


title: TGFBR2_M1V_TGF-β1_0h


title: R059-Combo1


title: Sham Unbound-R3

source_name: Sham Unbound, kidney

value: Mixed background

value: Kim1-GCE+/-; EGFPL10a+/-

value: Sham


title: SMAD3_P180Tfs*7_TGF-β1_24h


title: spleen_mouse_4_virus_2_techrep_1


title: kidney_mouse_2_virus_1_techrep_0


title: DIPG6-Pano2


title: Sham Unbound-R2

value: unbound (represents the total kidney)

value: Kidney


title: D2 IRI Unbound-R1

value: IRI


title: DIPG6-Pano1

value: Panobinostat


title: spleen_mouse_2_virus_2_techrep_1

value: tissue tropism screen

value: AAV genome DNA


title: heart_mouse_2_virus_1_techrep_0


title: SMAD3_P180Tfs*7_TGF-β1_2h


title: Sham Unbound-R1


title: spleen_mouse_3_virus_2_techrep_1


title: SMAD3_P180Tfs*7_TGF-β1_0h


title: DIPG6-Mar2


title: SMAD3_P180Tfs*7_TGF-β1_6h


title: spleen_mouse_1_virus_2_techrep_1


title: D14 IRI Bound-R3

source_name: D14 IRI Bound, kidney

value: bound (cell-type specific)


title: heart_mouse_1_virus_1_techrep_0


title: Patient3-TGF-β1_24h

value: JNK1 deficiency


title: DIPG6-Mar1

value: Marizomib


title: kidney_mouse_1_virus_1_techrep_2


title: spleen_mouse_4_virus_1_techrep_1


title: D14 IRI Bound-R2


title: Patient3-TGF-β1_6h

value: skin fibroblasts


title: D14 IRI Bound-R1


title: spleen_mouse_3_virus_1_techrep_1


title: DIPG6-Control2

value: DMSO


title: DIPG6-Control1


title: D7 IRI Bound-R3

source_name: D7 IRI Bound, kidney


title: Patient3-TGF-β1_2h

value: TGF-β


title: spleen_mouse_1_virus_1_techrep_1


title: DIPG6-Combo2


title: Patient3-TGF-β1_0h


title: spleen_mouse_2_virus_1_techrep_1


title: DIPG6-Combo1


title: D7 IRI Bound-R1

value: 8-10 week


title: Patient2-TGF-β1_24h


title: Patient2-TGF-β1_6h


title: D2 IRI Bound-R3

source_name: D2 IRI Bound, kidney


title: D7 IRI Bound-R2


title: liver_mouse_2_virus_2_techrep_1


title: Patient2-TGF-β1_2h


title: DIPG13-ComboLow2

description:
poly(A)+ RNA-seq
DIPG13-ComboLow2

data_processing:
Mapping: RNA-seq with tophat2. Default parameters were used against hg19 reference genome
Bed files generated using bedtools bamtobed
bedGraph files were generated using bedtools genomecov, then converted to bigWig using UCSC bedGraphToBigWig
Gene expression: For RNA-seq, gene expression was counted using featureCounts against an RefSeq hg19 GTF without miRNA or snoRNA
Genome_build: hg19
Supplementary_files_format_and_content: FPKM, counts

treatment_protocol: Cells were plated at 200k cells/mL and treated with DMSO control, 50nM Panobinostat, 20nM Marizomib, 50nM Panobinostat and 20nM Panobinostat (Combo Low), or 100nM Panobinostat and 50nM Marizomib (Combo High) for 16 hours

value: 50nM Panobinostat and 20nM Marizomib


title: DIPG13-ComboHigh1

description:
poly(A)+ RNA-seq
DIPG13-ComboHigh1

value: 100nM Panobinostat and 50nM Marizomib


title: Patient2-TGF-β1_0h


title: liver_mouse_4_virus_1_techrep_1


title: Sham Bound-R3

source_name: Sham Bound, kidney

value: Mixed background

value: Kim1-GCE+/-; EGFPL10a+/-


title: D2 IRI Bound-R1


title: D2 IRI Bound-R2


title: liver_mouse_1_virus_2_techrep_1


title: DIPG13-Mar2

description:
poly(A)+ RNA-seq
DIPG13-Mar2

value: 20nM Marizomib


title: DIPG13-ComboLow1

description:
poly(A)+ RNA-seq
DIPG13-ComboLow1


title: DIPG13-ComboHigh2

description:
poly(A)+ RNA-seq
DIPG13-ComboHigh2


title: liver_mouse_3_virus_2_techrep_1


title: liver_mouse_3_virus_1_techrep_1


title: Control2-TGF-β1_24h

value: control


title: liver_mouse_2_virus_1_techrep_1


title: Sham Bound-R2

value: Sham

value: Kidney


title: DIPG13-Mar1

description:
poly(A)+ RNA-seq
DIPG13-Mar1


title: Control2-TGF-β1_6h


title: liver_mouse_4_virus_2_techrep_1

value: tissue tropism screen


title: Control2-TGF-β1_2h


title: Sham Bound-R1


title: DIPG13-Pano2

description:
poly(A)+ RNA-seq
DIPG13-Pano2

value: 50nM Panobinostat


title: liver_mouse_1_virus_1_techrep_1

value: AAV genome DNA


title: DIPG13-Pano1

description:
poly(A)+ RNA-seq
DIPG13-Pano1


title: Control2-TGF-β1_0h


title: blood_mouse_4_virus_2_techrep_1


title: Control1-TGF-β1_6h


title: blood_mouse_3_virus_2_techrep_1


title: Control1-TGF-β1_24h


title: Med13-MO case ES807

city: Research Triangle Park

first: Carmen

middle: J

last: Williams

state: NC

address: 111 T W ALEXANDER DR

institute: NIH/NIEHS

data_processing:
raw reads were mapped to mm10  GENCODE comprehensive gene annotation cDNA sequences using BWA default paired-end read mapping protocol
the reads that were not mapped in-pair were filtered out
total read count of each transcript was reported and normalized by EpiCenter
FPKM data were derived from the normalized read counts
Genome_build: mouse mm10
Supplementary_files_format_and_content: FPKM data in microsoft excel file format

source_name: embryos

extract_protocol:
Total RNA was isolated from 4 independent collections of 40 embryos/group using an Arcturus Pico Pure kit (Life Technologies) and amplified using Ovation RNA-Seq System V2.
mRNA libraries were constructed from 400 ng cDNA using Illumina TruSeq RNA Sample Prep Kits, version 2

tag: genotype/variation

value: MED13 knockdown

value: morpholino oligonucleotides targeting the Med13 transcription start site


title: Med13-MO case ES811


title: Med13-MO case ES809


title: DIPG13-Control2

description:
poly(A)+ RNA-seq
DIPG13-Control2


title: DIPG13-Control1

description:
poly(A)+ RNA-seq
DIPG13-Control1


title: Med13-MO case ES805


title: blood_mouse_2_virus_2_techrep_1

tag: tissue


title: blood_mouse_1_virus_2_techrep_1


title: Scr-MO control ES810

value: negative control

value: scrambled control morpholino


title: IL-17RC_Q138*_IL-17A_24h

value: skin fibroblasts

value: IL-17RC deficiency


title: Control1-TGF-β1_2h

value: TGF-β


title: IL-17RC_Q138*_IL-17A_6h


title: Scr-MO control ES808


title: Scr-MO control ES806


title: Control1-TGF-β1_0h


title: blood_mouse_4_virus_1_techrep_1


title: blood_mouse_3_virus_1_techrep_1


title: blood_mouse_2_virus_1_techrep_1


title: Scr-MO control ES804


title: blood_mouse_1_virus_1_techrep_1


title: IL-17RC_Q138*_IL-17A_2h


title: IL-17RC_Q138*_IL-17A_0h


title: Rep_virus_4_c_GEN00105098

description: sequencing of AAV genome to determine packaing effeciency

source_name: AAV Capsid

value: capsid packaging screen


title: IL-17RA_Q284*_IL-17A_24h

value: IL-17RA deficiency


title: Rep_virus_4_c_GEN00105094


title: IL-17RA_Q284*_IL-17A_6h


title: P3_TGF-β1_24h

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The data were analyzed with R with RMA normalization

source_name: dermal fibroblasts

label_protocol: Standard Affymetrix protocol

growth_protocol: Dermal fibroblasts were cultured in DMEM supplemented with 10% FBS

extract_protocol: Total RNA was extracted with the RNeasy Plus Micro Kit from QIAGEN

treatment_protocol: Cells were left untreated or treated for 2, 6, or 24 hours with TGF-β1 (10 ng/ml)

value: dermal fibroblasts

value: patient with chronic mucocutaneous candidiasis and connective tissue disorder

tag: mutation

value: treated with TGF-β1 for 24 hours


title: IL-17RA_Q284*_IL-17A_2h


title: IL-17RA_Q284*_IL-17A_0h


title: P3_TGF-β1_6h

value: treated with TGF-β1 for 6hours


title: P3_TGF-β1_2h

value: treated with TGF-β1 for 2 hours


title: P2_TGF-β1_24h


title: Rep_virus_15_e_GEN00105090


title: Patient3-IL-17A_24h

value: JNK1 deficiency


title: P2_TGF-β1_6h


title: ChIP-seq of WCE [wt-RNAPIIser2P]

description:
Sample grown at 32°C, whole-cell extract, sequenced on MiSeq platform
Dhp1GFP_swd22∆ INPUT

source_name: log. growing cells

value: WCE, swd22delta cells


title: Rep_virus_14_d_GEN00105089

value: AAV genome DNA


title: Patient3-IL-17A_6h


title: Rep_plasmid_15_p-a_GEN00105088

source_name: DNA plasmid


title: P3_TGF-β1_0h

value: untreated


title: Patient3-IL-17A_2h


title: ChIP-seq of Dhp1-GFP from swd22∆ cells

description:
Sample grown at 32°C, additional crosslinking was performed with DMA for 45 minutes at room temperature in addition to formaldehyde, and was sequenced on NextSeq 500 platform
Dhp1GFP_swd22∆ IP

value: Dhp1-GFP in swd22delta cells


title: Rep_virus_3_c_GEN00105097


title: ChIP-seq of WCE [Dhp1GFP_wt_INPUT]

description:
Sample grown at 32°C, additional crosslinking was performed with DMA for 45 minutes at room temperature in addition to formaldehyde, whole-cell extract, sequenced on NextSeq 500 platform
Dhp1GFP_WT INPUT

value: WCE, WT cells


title: C2_TGF-β1_24h

value: healthy control


title: Patient3-IL-17A_0h

value: skin fibroblasts


title: Rep_plasmid_14_p-a_GEN00105087


title: P2_TGF-β1_2h


title: H1 DF IWP2

city: Macau

first: Ren

last: Zhili

address: Avenida da Universidade

institute: University of Macau

hyb_protocol: cRNA was hybridized onto HumanHT-12 v4 Expression BeadChip (Illumina) using standerd protocol.

scan_protocol: BeadChips were scanned with the iScanner (Illumina).

data_processing:
Data was normalized by quantile normalization.
www.arrayanalysis.org computed the normalized signal intensity.

source_name: Human embryonic stem cell H1

label_protocol: RNA was converted to cRNA using the TargetAmp™-Nano Labeling Kit for Illumina Expression BeadChip (Epibio).

growth_protocol: The differentiation process was performed on matrigel-coated plates with daily medium change.

extract_protocol: Total RNA was isolated by Qiagen Rneasy kit.

treatment_protocol: Control (ctrl): differentiation basal medium. IWP2, LY294002, insulin, IWP2+LY294002 were applied from day 2 to day 5 after CHIR99021 induction. The cells were harvested for analysis on day 10

tag: cell line

value: embryonic stem cells

tag: protocol


title: H1 DF INS

tag: treatment

value: INS


title: P2_TGF-β1_0h


title: ChIP-seq of Dhp1-GFP WT cells

description:
Sample grown at 32°C, additional crosslinking was performed with DMA for 45 minutes at room temperature in addition to formaldehyde, ChIP was performed using anti-GFP (ab290) and was sequenced on NextSeq 500 platform
Dhp1GFP_WT IP

value: Dhp1-GFP in WT


title: H1 DF IWP2+LY294002


title: C2_TGF-β1_2h


title: C2_TGF-β1_6h


title: C2_TGF-β1_0h


title: Rep_plasmid_0_p-c_GEN00113850

value: capsid packaging screen


title: Wt25_mRNA_Rep2

description:
WT25 RNA-seq Rep2
DEG.xlsx

source_name: mESC

value: embryonic stem cells stage

value: mixed C57BL/6J-129V background

value: wild type Tet3


title: H1 DF LY294002


title: C1_TGF-β1_24h

value: dermal fibroblasts

value: treated with TGF-β1 for 24 hours


title: Rep_plasmid_0_p-b_GEN00113849


title: ChIP-seq of WCE [WT_input]

description:
Sample grown at 32°C, additional crosslinking was performed with DMA for 45 minutes at room temperature in addition to formaldehyde, whole-cell extract, sequenced on NextSeq 500 platform
Iss1GFP_Input


title: Patient2-IL-17A_6h

value: JNK1 deficiency


title: C1_TGF-β1_6h

value: treated with TGF-β1 for 6hours


title: ChIP-seq of Iss1-GFP from clr4∆ cells

description:
Sample grown at 32°C, additional crosslinking was performed with DMA for 45 minutes at room temperature in addition to formaldehyde, and was sequenced on MiSeq platform
Iss1GFP_clr4∆ IP

value: Iss1-GFP in clr4delta cells


title: H1 DF Ctrl

value: Ctrl


title: CMV_virus_2_b_GEN00105102

value: AAV genome DNA


title: Patient2-IL-17A_0h


title: ChIP-seq of input in WT cells

description:
Sample grown at 18°C for 3 days, whole-cell extract, sequencing libraries were size-selected for 300-400bp fragments using AMPure beads prior to sequencing, and was sequenced on NextSeq 500 platform
input_H3K9me2_18C

value: WCE, WT cells


title: Patient2-IL-17A_24h


title: CMV_virus_2_a_GEN00105100


title: Control2-IL-17A_6h

value: control


title: ChIP-seq of H3K9me2 in ssu72∆ cells

description:
Sample grown at 18°C for 3 days, ChIP was performed using anti-H3K9me2 (ab115159), sequencing libraries were size-selected for 300-400bp fragments using AMPure beads prior to sequencing, and was sequenced on NextSeq 500 platform
ssu72∆_H3K9me2_18C

value: ssu72delta cells


title: CMV_virus_2_a_GEN00105096


title: ChIP-seq of H3K9me2 in wild-type cells

description:
Sample grown at 18°C for 3 days, ChIP was performed using anti-H3K9me2 (ab115159), sequencing libraries were size-selected for 300-400bp fragments using AMPure beads prior to sequencing, and was sequenced on NextSeq 500 platform
WT_H3K9me2_18C

value: wild type cells


title: Control2-IL-17A_2h

value: skin fibroblasts


title: CMV_virus_1_b_GEN00105101


title: Control2-IL-17A_0h


title: CMV_plasmid_0_p-c_GEN00113848


title: ChIP-seq of Iss1-GFP from WT cells

description:
Sample grown at 32°C, additional crosslinking was performed with DMA for 45 minutes at room temperature in addition to formaldehyde, and was sequenced on MiSeq platform
Iss1GFP_WT IP

value: Iss1-GFP in WT cells


title: Rep_plasmid_0_p-a_GEN00105091

value: capsid packaging screen


title: RNA sequencing of ssu72[delta] cells

data_processing:
Reads were quality trimmed using Trimmomatic and aligned using the STAR aligner to produce uniquely mapping reads, normalized to reads per million (RPM).  Aligned reads were assigned to transcripts on the basis of Pombase annotations using Rsubread. DEGseqwas used to compute the log2 fold-change in transcript expression between experimental strains and previously published WT grown at 30°C (Gallagher et al. 2018). Data for WT grown at 30°C can be found at GEO Omnibus accession numbers GSM2803075 and GSM2803077.
Genome_build: asm294v2.29
Supplementary_files_format_and_content: txt from DEGseq

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA). Cultures were grown at 18˚C for 3 days and maintained in mid-log phase.

extract_protocol:
RNA was extracted using MasterPure Yeast RNA purification kit (MPY03100, Lucigen) according to manufacturer's recommendation.
ScriptSeq v2 RNA library prep kit (Epicentre, SSV21124) was used according to manufacturer's recommendation.
Libraries were analyzed using an Agilent 2100 BioAnalyzer (Agilent) and sequenced on the Illumina NextSeq 500 platform.

treatment_protocol: Genomic deletions of swd22, ssu72, and clr4.


title: Control1-IL-17A_24h


title: C1_TGF-β1_2h

value: healthy control

value: treated with TGF-β1 for 2 hours


title: CMV_virus_1_a_GEN00105095


title: Patient2-IL-17A_2h


title: Control1-IL-17A_6h


title: Control1-IL-17A_2h


title: CMV_plasmid_0_p-b_GEN00113847


title: RNA sequencing of swd22[delta] cells


title: RNA sequencing of WT cells

value: wild type


title: CMV_plasmid_0_p-a_GEN00105092


title: ChIP-seq of H3K9me2 in swd22∆ cells

description:
Sample grown at 18°C for 3 days, ChIP was performed using anti-H3K9me2 (ab115159), sequencing libraries were size-selected for 300-400bp fragments using AMPure beads prior to sequencing, and was sequenced on NextSeq 500 platform
swd22∆_H3K9me2_18C

value: swd22delta cells


title: Control1-IL-17A_0h


title: CMV_virus_1_a_GEN00105099